There is a proper order to fill the slots on the original Mac Pro. You always install in pairs and are supposed to install in the slots nearest the logic board first. So the first two slots on the top riser should be filled first, then the first two on the lower riser, then the other two on the top riser, then the last two on the bottom.
Failing to fill the slots in this order may result in errors and will almost certainly result in reduced performance.
If you have filled one riser and the other is empty, then you need to put your new RAM in the two slots nearest to the board on the other riser.
There is a utility that usually complains if you have done it incorrectly. Maybe thats for the newer models.