It may seem difficult to set up but it actually isn't. Basically the analog stick in the middle of your N64 will be your PS3's left analog stick. The only tricky thing is, is the fact that the N64 controller has 9 additional buttons (not including the directional pad or start and select buttons) while the PS3 has 8 (9 including the PS button) but if you want to use the PS button then remember that you won't have excess to the XMB. So a simple reset can fix that.
Edit: Whoops, forgot about L3 and R3, so the PS3 has enough buttons on it for the use of N64 games.