If you know the Username or PNID of the user you want to add, type it into the Wii U Friends List app. (the orange smiley face on the home screen.) If you see someone online you want to add, you should make a note of their PNID.

It's probably the same for 3DS but I haven't used 3DS online multiplayer or added anyone on 3DS for a long time. But I'm pretty sure you go into the Friends List and type their friend code into your 3DS.