theaero, I'm not sure weather it's a question or a statement. I modded my wii some years back. I only use Sd cards for the initial hack. Then as you say everything else is on the root of my HDD. I use Wiimc, USB GX Loader, CFG Loader, CE Player and BBC IPlayer. Depending on how you configure your system I guess. Read the site thoroughly I'm sure certain things will need you to keep an SD card in the slot.
ENJOY YOUR WII