From what I’ve been reading at CreativeCOW and elsewhere, the current generation of MacBook Pros and Mac Pros use a single FireWire bus for the 1394a and 1394b ports. Thus, attaching a FW400 and FW800 device simultaneously will cause both to operate at FW400 speeds.
Putting this in the context of Final Cut Pro, it’s not an issue with SD footage because FW400 has plenty of bandwidth. A forum topic at CreativeCOW suggested that HD content be edited on eSATA drives but I’ve used ProRes422 files on FW400 without any problems. Mind you, cutting not capturing.
If separate buses are required, outfit your Mac Pro with a FireWire PCI card or in the case of the MacBook Pro use an ExpressCard.