Hey there,
I’ve been in this position before. I’m an editor not a shooter and I’m used to the shoulder cam xd cameras not the EXs. If the footage has already been shot… your really going to be in a tough position. My best suggestion would be to drop all clips from each disk into their own sequences, and name the sequences disk1, disk2 etc… I had to do this in Haiti, and it’s a major pain in the butt… however it’s easier than dealing with a bajillion clips.
Now I don’t know where in the menu it is because I’m more an editor than a shooter… but there are modes you can select. I always ask my cameramen to shoot in ‘multi-clip’ mode. This creates a new clip every time the camera is turned on and off instead of on each record. I think you can even arrange it to give you FCP markers on each record press.
Sorry I don’t know the menus, but search around for multi-clip… there is an answer.