Ok to have one riser card empty?

Maybe we have to back track here for a second. Yes it ships with ram in each raiser. But it is suggested to extract the ram from the bottom raiser and install in the top raiser so you have a matched pair of ram on one raiser.
I have linked a video here for you to watch that will be helpful if you choose to take apples recommendation.
Good luck hope this helps.

http://eshop.macsales.com/tech_center/index.cfm?page=Video/macproearly08/memory/ low.html

As soon as you can afford to, add more memory.

System Profile: Memory

Run Apple Hardware Test is a good idea with any new system.

2GB is the minimum, whether as it shipped or moved to top Riser.

http://www.barefeats.com/harper3.html

Hmm. Why would Apple put them on separate risers if they're better off on the same one?

The Mac Pro has separate branches of the memory controller for each riser.
<http://developer.apple.com/documentation/HardwareDrivers/Conceptual/HWTech RAM/Articles/RAMimplementation.html#>

With only two memory modules:

On different risers, it can simultaneously access two 64 bit words at different addresses if they are in different modules.

On one riser, the two modules act as a single 128 bit unit. It can access 128 bits at once, but they have to be adjacent. If it doesn't need more than 64 bits, one module is being wasted for that memory cycle.

So, with the modules on different risers, there are more opportunities for both to be used simultaneously.