Word gloss issues

I am interested if we enter base or inflected word form in the word gloss line?

Great question… Since this is a “word gloss”, rather than a “lexeme gloss”, it should be inflected to match (as much as possible) the inflection of the surface form, or “word base”. The lexeme gloss should be uninflected. At least… that is how I have understood/used it.

Training | SIL Mexico has two papers on glossing in FLEx (in Spanish).
Section 7 of Guía básica para glosar textos con FLEx | SIL Mexico gives two options: popular glossing and technical glossing. In a simple example, “walking” could be glossed as “caminando” (popular) or “caminar:PRT” (technical, where “PRT” is short for “participle”). Your team will have to decide this, considering your goals and your audience.

To take advantage of the Lexicon, split the words into
Morphemes: walk-ing
Lex. Gloss: caminar-PART