I assume you are playing the gamecube version using Nintendont as the Wii version is only on one disc.
For 2-disc games on nintendont you should create a subdirectory /games/MYGAME/ (where MYGAME can be anything), then name disc 1 as "game.iso" and disc 2 as "disc2.iso"
When you finish disc 1 the second disc will automatically be loaded and your game will continue.
On a side note why are you not playing the Wii version of Resident Evil 4 it has many more features and extras including a whole separate story for Ada and can even be played with a Gamecube controller.