It's really quite simple: there must be exactly two ends of the SCSI bus and both must be terminated. Active termination is recommended, but on Fast SCSI you can also use passive terminators.
Of course, each of these ends may be the controller (HBA) or a drive, or the terminator may be integrated into the cable end or an external type. If you use both connectors on the HBA (internal and external), termination must be deactivated because the board is in the middle, not at one end.
Everything else, i.e. 'multiple chains' is complete crap. It might work, but it also might fall over tomorrow. I've seen quite a bit of messed up setups - some of them even working, but if you changed one single bit you were bust - that's where I was called usually. So better make it right from the start.
@ral-clan: if the resistors are soldered in, you can't use both connectors simultaneously. There are only two solutions: desolder and socket the resistor packs or use an internal/external adapter at the other end of the cable (disable term on all internal drives, of course). When the new external connector is not in use, use an external terminator plug.
