Congrats on your new long arm quilting set up. It is an exciting thing for a quilter to get one!
I have an HQ16, no stitch regulator, on a frame. (I use the pcquilter, a computerized system to "do" the actual quilting.) In general, the thicker the sandwich, the less depth for the quilting. Flannel, minkie and fleece are thicker than most 100% cotton quilting fabric, so take up more room on the take up rail/in the throat of the machine.
The same is true for batting. The thicker it is, the less depth you have for quilting on the frame. Batting that I use is Hobbs 80/20, not too thin and not too thick.
Note: for a variety of personal reasons, I only do end to end quilting. If you intend to do more customized quilting, the numbers I'm giving may not work for you.
Having said all that, and considering that most of the quilts I quilt are 100% cotton with the Hobbs 80/20 batt:
For larger quilts, over 70 inches long, you are probably best off allowing no more than 10 inches of depth for quilting/in the throat of the machine.
For a baby or toddler quilt, which I define as 40 - 50 inches long, I have gotten away with a 12 inch depth for quilting, but generally allow myself only 11 inches of depth to quilt in.
Lap quilts, 50 - 70 inches long, at most 10 - 11 inches of depth for quilting.
Happy quilting!