This Perspectives article discusses how you should teach your child to decide whether he's encountering either a new phonogram in an word, or an unusual pronunciation of an existing phonogram, or just another one of those occasional weird spellings that he has to memorize in that particular word.
As discussed in an earlier article, one of the attributes of a phonogram marking system should be that "the logic underlying the phonogram set should be easily, and logically, extended to phonograms not included in the set." Another attribute was that the marking system "should accommodate an easy-to-learn method for describing the inevitable exceptions to the underlying logic that are bound to occur in some English words."
There are two situations that will typically occur. 1) An extraneous letter appears in the word, but is it really extraneous, or is it part of a new phonogram? 2) A known phonogram represents an unusual sound, but is it really unusual, or will it be encountered again and again as one's reading level increases?
The Initial Approach
The first time a new situation occurs, the double-underline should be deployed, whether the situation involves a new sound being attached to an existing phonogram, or an extraneous letter appearing in the word.
Taking the case of an existing phonogram, consider the word plaid. The phonogram ai has been taught as /ae/ already, and depending upon how he considers words like said, again, against, mountain and captain, he might already have added a second option, the /e/ sound, to the phonogram ai. Should it now also be considered a spelling of the /a/ sound, as it is in plaid? You really don't need to know the answer, nor does your child. What you do need to know is that, so far, it hasn't been taught as representing the /a/ sound. Therefore, it's an unusual pronunciation for the phonogram ai. All your child need to do, then, is double-underline the phonogram ai, and write "a" under the lines to remind him that this is the /a/ spelling in plaid, but that it's unusual and must be memorized.
Later on, should he run into another word that he ends up treating the same way (though I can't think of one offhand), he should do the same thing, but also ask the question, "Hmmm, this is twice now that ai has been the /a/ sound. I wonder if this will keep happening?" Between you and your child, set some minimum number of occurrences before you both think of /a/ as an acceptable sound to be associated with the phonogram ai. My personal number is three, but only in words that I would normally encounter while reading, not by going to a medical dictionary, or a list of weird crossword puzzle answers. After all, the purpose of building a working set of phonograms is to enable your child to decode unfamiliar words that he is likely to encounter in his normal reading.
How About a Potential New Phonogram?
You and your child will both run into phonograms not included in the initial teaching set of 84 phonograms. Some of these will be obvious, like the phonograms ss, ll, and ff in grass, ball, and stuff. The split vowel digraphs like the i-e in ride also aren't in the 84-item set, but are taught as extensions of the phonograms ee, ie, oe, and ue. (And the a-e in fame is just a further extension of those.)
But what about the "the" in soothe? Is there a phonogram the, or should the letter "e" be double-underlined as an extraneous letter? The beauty of this marking system is that you can change your mind as additional information filters in. If this is the first time your child, or you, have ever encountered a word where you find yourself asking if "the" is a phonogram for the /the/ sound, rather than decide immediately, just double-underline the letter "e" and put a 2 over the digraph th. Thus, the word soothe is marked as s oo th e (with a 2 above the phonogram th and the letter "e" double-underlined as an extraneous letter.)
Your child will might later run across the word clothe, and follow the same procedure as with soothe, but will begin wondering if a phonogram the exists, one that appears to represent the /the/ sound. Do you see how this process of discovery primes your child to be able to deal later with writhe or lathe when they appear in his reading? He will be thinking about it, and the act of discovering it on his own will do far more to cement his knowledge of the phonogram the than explicitly teaching it in advance would ever do.
By the time he runs across the word absinthe, he will be single-underlining the phonogram the (for he's convinced himself that it is a phonogram for the /the/ sound) and will be wondering if he should adjust his thinking to add the /th/ sound as a second option?
Unusual Beginning Digraphs
There are a few cases where it's easy to determine whether a previously unseen letter combination should be considered a phonogram. They occur at the beginning of words a lot. For example, if your child is reading about pterodactyls from the dinosaur era, he might wonder if "pt" is a phonogram for the /t/ sound. Going to a dictionary would convince him it is, as he'd find several dozen words that start with "pt" pronounced as the /t/ sound. In fact, with the internet, locating words with any letter combination within a word is now easily done.
However, there is a reason to discourage this sort of search, in favor of letting the normal process of discovery proceed as described above in the case of the phonogram the. Remember, you're teaching your child a working set of phonograms. If you look at the list of words beginning with the phonogram pt, you'll see very few that a child under age 10 will ever run across. So if you introduce a phonogram pt, or if you encourage him to go looking for it at the age of 7 or so, are you really doing him a favor? Remember, he's going to encounter all sorts of words with the spelling "pt" (apt, aptitude, option, caption, uptown, etc.) but do you really want him to be considering a phonogram pt in those words? Of course not, because in each case the phonogram p stands alone, and represents the /p/ sound, while the phonogram t that follows represents the /t/ sound. You really don't want to encourage him to isolate pt as a phonogram at that age.
Adding in the unusual phonograms before your child discovers them in the course of his normal reading risks causing more confusion than clarification. Consider that before forging too far ahead of his reading level in the search for every possible phonogram, and every possible pronunciation option. Stick with the double-underline until your child begins to question it in a given situation, and his questions will accelerate the learning of the less common phonograms.
Handling the Inevitable Disagreements
By "disagreement," I mean with the curriculum, not with your child. Some people will never be able to convince themselves that a word like ago can easily be taught as beginning with an /o/ sound. They'll continue to insist on teaching it as an /u/ sound. Fortunately, the marking method allows for that eventuality. Just double-underline the phonogram a the first time it occurs, and write a "u" under it for the /u/ sound. By the third time it happens or so, add /u/ to the /a/ae/o/ pronunciations. Of course, now you have to run through four options, /a/ae/o/u/, but it would work.
Many people might prefer to do this with the phonogram ai, for example. I always preferred to treat said as the exception, and for spelling purposes teach a child to think of again, against, and words ending in tain like mountain, captain, and fountain, as having /ae/ sounds, but adding the /e/ sound after running into several examples is certainly an option. (Just don't also add /i/ for the words ending in "tain." At least get your child to think /e/ in those words. After all, it's really just a schwa. Don't make the mistake of adding yet another sound to the phonogram.)
And, finally, dialect differences across states, regions, and countries will inevitably cause disagreements with the phonograms as presented in the 84-item set. Those, too, can be handled the same way, deploying the double-underline at first, then modifying the phonogram structure as you go along. The point of the entire exercise to build a working set of phonograms that a young child can use to decode the thousands of unfamiliar words he will soon encounter. Don't lose sight of that.