Add roms to iso file is not possible (well... is possible, but emulator cant find them).
Its easy to do all of this. You need
Marcam iso template.
Wiiscrubber
Partition Builder
Wii iso title Renamer
Hexeditor
Your new main.dol (boot.dol)
1-Extract files from marcam iso template using wiiscrubber.
2-With an hexeditor edit boot.bin. You will see iso ID at the begining, followed with iso name. Replace it with your new values.
3-With partition builder generate a new partition using files extracted from step 1 and step 2. Using your own main.dol
4-With wiiscrubber, load iso template, then load partition generated on step 3. You will see the new values changed on step 2. (close wiiscrubber)
5-With Wii iso title Renamer change the game id and game name (thats the values displayed on WBFSManager)
Thats all easy, isnt it?