You could try wetting the sandwich you already made to spread the glue out. Get it nice and wet and then press it; that might spread the glue enough that you could sew over it easily. Press straight down, don't sweep the iron over the fabric, so you don't mess up your alignment. Probably good idea to put a towel over & under it to pick up excess water.
Then again, I've FMQ'd through some pretty big blobs and my machine didn't seem to notice. You might want to just give it a shot as-is.
