Merging is a bit of a pain sometimes. It depends on how nice the creator was really. Some come with a modified file list that lets you tell exactly what was edited, if both mods have this then its a far simpler task of copy and pasting from one mod into the other of all the mod files. If they didnt give you a modified files list then its a bit more work as you have to find these yourself and hope you got it all right when you copy and paste over.

As for mods that would be best merged together, its really up to what you want from the mod. Some of the better merges are visual (as long as they dont overlap that is!) with one type of combat/research changing mod. Mini mods (like max fleet size 10k, additional capital ships, lowered fleet upkeep) would/should also merge well