I use glue basting and never have globs so I'm not sure how you're doing it. I hold the glue bottle fairly high above the quilt bat and a thin stream will start to run out and then I just make zig zag motions with the thin stream. If I do get more than I want in a space, usually when I start or stop, I just smooth it out with my finger. I've never had a problem with a sewing machine needle going through the layers with glue basting. You don't need much glue for it to work.
I use Warm and Natural batting which is 100% cotton with scrim. I believe that polyester batting is more prone to shifting and might produce more wrinkles.
I sandwich in sections on a small table. I put the batting down first, squiggle the glue on it and then smooth the backing over that. You can readily see any wrinkles and smooth them out with your hand. I don't have to clamp the batting down because it is thicker and stays relatively stable throughout the process. When that section is dry I move the batting and back, fold the back the backing and repeat the gluing process. When I'm done with the back I flip the whole thing over and repeat the process with the front.
When I'm working on a smaller surface I will mark the center point both vertically and horizontally with straight pins of the batting, backing and top and match those up to center my batting and backing and eventually my top so I don't end up with things lopsided.
The thing that made sandwiching so much easier for me was not having to have all three layers together at the same time like you do with thread or pin basting and having either the back or front of the quilt which has thin more slippery material against the smooth slippery surface of a table. By putting the batting down first which is more stable and then putting the other on top of that was a real life changer for me.
I'm young enough and agile enough to crawl around on the floor but I choose not to do it. It is so much easier and more fun to not do it on the floor. You don't need a big surface to baste.