Nope, don't put any gravel on the bottom. It just traps poop and other debris, and harder to clean. Good idea making them some hiding spots. They will get more friendly as time goes on, unless something scares them constantly.
I have two pumps in my ponds. One runs my skimmer and whatever I run with the skimmer outlet (pump pulls water through the skimmer, and then sends it out to something else - waterfall in one pond, stream in the other pond), and the other pump is on a milk crate on the bottom, running the bogs. My skimmer pumps are 1600 gph each. The larger pumps are 4200 gph. The main thing about a pump is you want it to circulate your total gallons of water at LEAST once an hour, best if 1.5 times or even 2 times an hour. More circulation is better.