I am very new to longarm quilting too but I say yes, batting changes do affect the stitches. I found this out very quickly when I tired to use very cheap lofty batting to practice when I first got my machine. Didn't want to waste good batting. But I was very frustrated with the outcome - horrible tension issues, etc. Changed to good batting and all problems were fixed. A couple of long frustrating days before I tired it. I will never use cheap batting again. I like the warm and Natural or Hobbs 80/20.