No. don't put 'em in!! Trust me in that I'm saving you from hell. People think rocks in a pond look pretty and natural. However, that pretty and natural look will end in a few months when you've got debris laying in every crack and crevice you can't remove.
Just keep bare liner. that is all. It's a captured body of water--you try to make it look as natural as you can...but at the end of the day it's a big hole with fish in it and you need to keep it clean. So, don't make the cleaning aspect harder than it should be. Keep your floor bare....
Of course, if you want to put rocks around the outer edges of your pond, by all means, go nuts. Just NOT inside the pond.