The short answer
Students aren't expected to know until you tell them.
While knowing the phonograms and their sounds lets you know exactly what your options are, and the spelling rules greatly narrow the number of choices a student must consider in determining how to spell a particular sound, sometimes more than one spelling is permitted by the rules.
In the case of EE and EA, for example, no rule dictates which may be used where. In fact, we often have homophones differentiated by two different spellings of the same sound, such as peek and peak, meet and meat, or see and sea. This happens with other spellings too, such as toe and tow.
How does this work, then?
Whenever there is more than one permitted option, the teacher always needs to cue the student on which phonogram to use during the process of spelling dictation and analysis. The student cannot be expected to know. The purpose of Spelling Analysis and the spelling lists in Essentials and Foundations is to teach spelling, not to test it, and whenever information beyond the spelling rules and phonograms is needed to guide the student in choosing which phonogram to use, the teacher needs to provide it.
Where can I learn more about how this works?
If you are using Essentials, a detailed guide to the process of teaching spelling words through Spelling Analysis, including how and when you should cue which phonogram to use to spell a particular sound, is found in the introduction. (In the current edition, this is in the beginning of the 1-7 Teacher's Guide. If you are using a previous printing of Essentials, you'll find it in the introduction to the Essentials Volume 1 Teacher's Guide and the 1st Edition Essentials Teacher's Manual.)
The Spelling Analysis Card is a helpful guide to the steps for teaching Spelling Analysis.
Video trainings: Watch video trainings by Denise Eide on how to use Finger Spelling, a simple but powerful tool for cuing phonograms, and how to teach Spelling Analysis. You can also watch Denise model the process in Spelling List 3 and other Spelling List videos on our video page.
How do students master words that have more than one option for one of the sounds?
In Foundations, memorizing the spelling of individual words is not a priority, since the focus is on equipping them with all the tools to read any word and understand how English spelling works. Learn more about spelling in Foundations.
However, it's important to master individual words eventually! This becomes a greater focus in Essentials. Step one is learning a word through Spelling Analysis, since this gives students a deep understanding of how it is spelled and why (and builds the skills they need to spell other words fluently). However, the process doesn't stop there.
Once a student has learned the spelling of a word through spelling analysis, the Spelling Journal provides a place to record difficult words and keep track of the different ways of spelling a sound.
Spelling games and other spelling activities in Essentials lessons provide various opportunities for practice with the words students are learning. Students also practice their spelling words while working on the Grammar sections of Essentials lessons. Eventually students also practice their spelling words through Dictation. This is the most challenging form of spelling practice, as well as the one that most closely mirrors real-life writing, since it requires students to spell correctly while holding a complete thought in their heads and thinking about punctuation and how to put the whole sentence on paper rather than one individual word.
Essentials lessons also guide students in understanding which of the permitted spellings of a sound are more common in different places within words. For example, Lesson 2 guides students in discovering where CK may not be used, where it may, and where it is the most common spelling of the sound /k/.
However, keep in mind that it takes time and practice to master a tricky spelling; if a student doesn't remember, simply prompt her again with the same cues from spelling analysis and move on.