I've pieced long & short strips of left over batting together with a very large zig zag stitch, and have had NO problem with it being puckered, or anything else bad.I am a hand quilter. However, I've not quilted on a long arm, just FYI. I also have used small left over pieces of batting that are nice sized for placemats; potholders; small quilted purses; etc.
I'm proud of you for being 'green'! Old saying 'waste not, want not!'