Parts of speech and roots and affixes can be learned concurrently over the two years. I believe the best results are obtained by committing the parts of speech and their characteristics to memory, and then continuing to review throughout the two year period. Use increasingly complex sentences from their reading to practice identifying parts of speech. And drill, drill, drill the classifications of words. In teaching roots and affixes, present the concept of roots first, then suffixes and their meanings.
Many suffixes change the part of speech a word occupies in a sentence.
For example, the suffix -able changes a noun, such as peace, to an adjective, such as peaceable. Give plenty of practice in manipulating words by adding all manner of suffixes to roots. The rules governing spelling of words when adding suffixes can be thoroughly covered in these two years. Then proceed to the adding of prefixes, all the while continuing to review the suffixes. Prefixes do not change the part of speech of a word, but the meaning of a word.