The 25-pin external scsi port uses the macintosh unofficial scsi pinout. They used the DB25 connector because it was smaller than the official connector. Commodore went along, I suppose because it was a defacto standard by then. Anyway, the internal and external scsi ports are directly connected - they are on the same scsi bus. (half of the pins on that internal connector are grounds..)
There is a set of terminator resistors on the motherboard. Normally, the scsi bus is supposed to extend from one terminated end to the other, with no branches. However, it is permitted to have a short stub off the bus. Like the distance between the SCSI chip and the terminators themselves. ... or the cable between the motherboard and the internal drive. Those motherboard terminators can be considered as being on the internal drive... (assuming you don't have more than a few inches of cable to the drive)
The problem comes in if you have external scsi devices. The last one of those will have termination. If you had the internal drive terminated, that would put two terminatons in the computer... a no-no. Ideally, in that case, you should remove the terminators on the motherboard and put terminators on the internal drive. But the motherboard terminators are not removable.
I seem to recall that the 3000 came with an external terminator. That would put the termination on the other end of the bus.
Clear as mud, eh? :-)
