Put everything in the same folder - isos, make-multiv3.exe, GCMUtility, and newly created .bat file.
Download the latest multidisc maker v3, not v2 - its included in the Wiikey setup disc 1.2.
Shrink each iso with GCMUtility v0.5 before making the multidisc (Google search it).
I'm assuming you have a USA modded Wii. So, for example, if you've got the isos Mario Kart DD.iso, Zelda WW.iso, and Pikmin 2.iso, shrink them with GCMUtility first.
Edit:
Rename the isos so that they contain no spaces, otherwise when running the program in DOS prompt, it will give an error of file not found.
It doesn't matter if the isos are mixed - PAL, USA, JAP, GCOS will let you output whichever region.
In notepad, type:
make-multiv3 multi.gcm mkartdd.iso zeldaww.iso pikmin2.iso
Save it as multi.bat in the same folder as all the files.
Double click the newly created multi.bat file, and it should create your multi.gcm file. You'll know when its finished when the DOS window is gone and your system is doing nothing.
Burn the multi.gcm onto a DVD-R/+RW with something like IMGburn, and play on the Wii.