Suppose its <ST>---<Link>---<Small Rodime>---<Large Rodime>
Remove the termination resistors from the small Rodime, and make sure that the large Rodime has them. I don't know what model your drives are, but older drives typically had three resistor packs right by the SCSI connector. If they are both coming up OK individually, I'm inclined to believe both drives have the termination resistors in place.
Next, you need to make sure that the drive ID's are set properly. If they are 0 and 1 (which you can verify either with the docs or seeing what they come up with when connected individually). 0 and 1 is fine, so long as they are different and not 7.
Then make sure your hard disk software is configured to look for drives at both those IDs. Again, if they both show up individually, you are probably OK, but it is something to be aware of.
Oh, The ID does not determine which drive is the boot drive, you set that in the software.