Kasey, are you planning to work them flat or working them in the round? Working a gusset is easier in the round. In fact, I've never seen a gusset worked flat. That doesn't mean it hasn't been done and can't be done, I've just never seen it done. You could easily make a space for an afterthought thumb if you knit flat and then seam the sides without leaving a hole for the thumb. And then work the afterthought thumb.
I would like to suggest you start this same discussion in the Ask the Fair Godknitters KAL. The reason being this is a group of knitters with all experience levels who aim to help those with all kinds of problems. I think more more active members would see your request there than here.
Leaving your discussion here is no problem, I just want more people to see it.