[Greg] “For example, whenever I hit open fle on Media 100, a list of documents open and I see all of the bin and program documents.”
When you create a new Bin or Timeline you need to save them somewhere. I would suggest copying the bins and timelines (wherever you have stored them) also to your FireWire drive. But yes, media files that are copied to a FireWire drive and back will relink to your timeline. If they do not relink automatically use the “Relink Media” command in the “Media” menu. Media 100 will search and relink to your media files.