Use the search function
I feel like being nice today:
It's actually not that complicated, it's just that there's multiple programs. I'll give you the down-low. The two best n64 emulators are 1964 and Project64. However, if you want to play online you need Project64k. 1964 is a better emulator and has more features, but Project64 is compatible with more games. (Though, when version 1.7 comes out that should change).
You have 3 plugins: Graphics, Audio, and Input. Graphics and Audio you should leave alone, but you need to set up your Input plugin. You can set it up to the keyboard, but if you have a gamepad you can set it up to that. Then you get ROMs and start playing!
For online play in Project64k, go to File-->Start Netplay. Then join one of the servers; Emularena Grounds has the far most n64 matches. Then just start or join a game!