I have System Commander as well. What it wants to do to laod linux is find lilo on the boot(right word?) sector of the partition linux is on, not the MBA of the whole disk. Lilo can be configured this way, but I'm not sure the Debian distribution has an option set up for doing it on install through the scripts. I am between distributions myself at the moment, when I get the time to put Debian on again (had 1.1 before buying a new computer) I think I'll just ditch System Commander in favor of lilo. It can load other OSs as well for you if you want.
I like six eggs when starting on a journey. Fried - not poached. And mind you don't break 'em. I won't eat a broken egg. -- Thorin Oakenshield