wii games go into /wbfs/ folder
gamecube games go into /games/ folder
you better use WiiBackupManager (windows) or
WiijManager (mac) (don't use it, it's wbfs only!)
Wiibackupfusion (mac) to put your wii games on your drive, it will rename and copy the file to the correct folder for you.
for gamecube, you'll have to do it manually, usually the best location is :
/games/<game's title> [<TitleID>]/game.iso
example :
/games/Luigi mansion [GLMP01]/game.iso
it's the same for wii games, except the iso is not named "game" but based on the titleID too :
/wbfs/game's title [TitleID]/TitleID.wbfs
Cluster size of 32k is always preferred for compatibility with older apps, even though 64k could speed up a little (very little) the read speed, and prevent lags in some games. but it all depend on your SD or USB speed. try 32k first.