I really love Glue-BasteIt by Roxanne. I get the EZ Squeezie bottle & it makes a perfect skinny line (or tiny dots) of glue every time. I've never had issues with it showing after it dries as long as I use cotton fabric. I've also used washable glue sticks (white, not purple -- though some people swear by the purple ones).
I think the Glue BasteIt would be the quickest secure route to go for machine stitching, but you could also just do a fusible. Instead of cutting everything in advance, here's what I'd do:
1) Iron Parchment Paper to my ironing board (or pin junk fabric to your board to protect it)
2) Place WonderUnder paper side down
3) Lay pre-cuts wrong side down on top of the WonderUnder
4) Place a Pressing Sheet or some parchment paper gently on top of the pre-cuts & tack together with an iron as per manufacturer's instructions
5) Peel off the Parchment Paper & cut out the fused fabric + fusible units
6) Peel off paper backing & fuse to your background fabric
The only time I wouldn't do that shortcut method is if you are using larger pre-cuts (3"+ wide and long) that would benefit from being windowed (cut the center out of the fusible, leaving only a generous 1/4" of fusible to press to inside edge of pre-cut). Windowing makes the finished product softer & gives it a better drape, especially with larger applique pieces. Nevertheless, I've done applique without windowing -- before I knew better -- and it still was a snuggly little baby quilt. You will save quite a bit of time if you don't have to window.