Ok great, thanks a lot for the help.

I'm working on a new problem now, in that I'm trying to use this system for real time control of a robotic system. I'd 
like to have a control loop run at say 1khz, and maybe a loop that checks the sensors at some other frequency, I'm very 
lost as to how to go about implementing this.

I can't really use the hardware counters/timers on the Sensoray 526 I have as I 3 of them for encoder inputs so I'd like
 to use another method. I find the documentation really lacking on how to go about doing this, should I use 
InterruptAttach()? InterruptAttachEvent()? have the clock send a pulse or message?

I can't find any really good documentation or sample code for this sort of problem. I know people are doing things like 
this and so it must not be that hard, but accurate loop timing is one of the reasons I decided to use the QNX RTOS.