Nathan-
A word of advice: There is *NOT* a good way to fill in the Word Glosses from the Lex. Glosses after the fact. So if you think you want to do text glossing in the future, I recommend leaving that line showing. You can just ignore it--if you fill in the Lex Gloss line, the Word Gloss line will get automatically populated, but only if it is showing. It may not be exactly what you want, but it will be something. But the way things are right now, it will be very hard to do text glossing later if the Word Glosses have nothing in them, unless you (or whoever is doing the charting) is so familiar with the language that glosses are not needed at all.
Regarding the conventions that Sarah asked about, yes, it completely depends on your goal and who you are doing the glossing for. If it is for a consultant, they will have recommendations. If it is for a publication, look at the conventions there.
In some situations, people do exactly what you gave an example of: They use grammatical glosses for the individual morphemes (like 3.dual) and real words for the word glosses (like "they.two") Others want a concatenation of the morpheme glosses.
Regarding using periods or spaces, again it depends on your output. In the Leipzig format, the convention is to put hyphens and no spaces between each morpheme gloss. In that case, it probably doesn't matter. (In this case, it is only at the word level that glosses are lined up across the rows. You don't get the morpheme gloss directly under each morpheme.) FLEx allows some output options where the "bundling" is by morpheme rather than by word. In this format, it is whitespace that tells you where the morpheme breaks are in the morpheme gloss line. In that case, it would be better not to include whitespace in your glosses, to avoid confusion.
In summary, there are pros and cons to each of the options mentioned, and it all depends on your audience and your goal.
-Beth