My advice for first time use is to use as few pins as you can get away with to make things easier, and play around with it in a new comp to get a feel. Many people I talk to don't even know about the puppet starch and overlap tools (click-hold on the puppet pin icon to show them) which are crucial to getting a mesh to behave the way you want. I also almost always increase the minimum mesh count for better deformation.
Also, chop things up if you can. If you're using Inverse Kinematics as well, you may already have done this. But it can be cleaner to animate one piece of your character at a time separated from parts that might not distort properly. On Red Vs. Blue season 10 we had to animate an alien Engineer (a floating turtle/snake like creature in the Halo universe) as a card we could project shadow imagery from in Maya. I built it up using parented objects that had puppeting applied to individual pieces. It was much easier than trying to starch certain pieces.
One of other super handy things is recording via the command key. hold command down and click one of your pins and use the mouse to animate it over time. You can build up some pretty complex animations pin by pin (and then obviously tweak the keyframes)
You can see the finished puppeted creature and the way it looked projected here: