I have the HD (on SCSIDE) mounted upside-down (circuit board up). This allows the slightly larger ACARD board to fit better. I also have a cable that includes an external wide SCSI connector so it made sense to route it that way.
I can't really help with the SCSI patch. I ended up putting my DVD/CD-RW combo on the onboard IDE because of problems getting the SCSIDE working, cable routing issues, and reading their documentation which mentions limited support for burners.
BTW, turn off any SCSI id's that you're not using, and set all LUNs to 1 (unless you're using a CD-ROM changer you won't need it). This will speed up the SCSI scan quite a bit.
