If you are installing this on the primary IDE cable and the cable is an 80-wire then the drive positioning is more important than a 40-wire.
The three connectors are as follows:
The connector farthest from the middle connector goes to the connector on the mother board
the middle connector is the one for the slave drive
the connector at the other end that is closest to the center connector is for the master drive
Since 80-wire IDE cables are wired specially the above is the only way that the drives will work properly and there is not diddly anyone can do about it.
As for the jumpers on the back of the hard drives this is another matter sometimes they do not work as they should since drives of different manufacturers have slight problems using these together when set supposedly in a proper way, the solution is to guess which way and this is tough I would suggest making a diagram and sritting the pins locations down when the shorting jumpers are applied.
It one took me three hours to figure the way the jumpers went but when the post booting sees the drives you should be set.