I'm not sure if I'm understanding with absolute clarity what your objectives are, so my response may not be the right one. Are you making entries for every inflected form (masc nom, fem nom, masc acc, fem acc, etc.), or are you using the masculine nominative form as representative for all of those? The latter is how dictionaries are typically done, but your use case may be different.
If you're wondering how to make a single representative entry for "nimble", it should look something like this:
The Lexeme Form field contains the stem, but since that form is nonsensical in isolation to a speaker of the language, the representative inflected form is entered in the Citation Form field. This provides a headword that native speakers recognize as a legitimate and well-formed word, while informing FLEx that the stem does not include the final "y".
The suffix -y would constitute a separate entry, where information is provided about which sort(s) of stem(s) it attaches to and in which position in the structure of the word, like this:
It is then possible to use this information to analyze words in texts into the constituent elements:
Does that help?
Kevin