So, I will log and transfer HD clips into FCP 6. and if I dont want them, I just simply highlight and delete them. But, where do they go from there? I empty my trash, but I'm still losing memory. I found my scratch disk so do I delete them from there? or is there an easier way?

right click (ctrl click) the clip(s) you don't want and choose "Make Offline" from the context menu (or choose "Make Offline" from the "Modify" menu) ... in the subsequent dialog choose "Delete Them From the Disk"