Ruby2shoes - perhaps you used too much glue? If you had so much you could use a scrape to spread it that may be too much. I think that has been mentioned here on the QB.
I've only used thin strips from the bottle a few inches apart. On small applique things I've used a school glue stick as it is very easy to apply. I've only used school glue on small applique projects so far but like how easy it is to use and soft after you are done. When I first started to quilt and read about pin basting I was immediately on the hunt for a longarm of some kind. I've done a few small projects with pin basting(before longarm) and hated every minute of it. Don't know how you stand doing a large quilt at all with pin basting.