Nice avatar!

You gotta love Franky!
If I understand your application, then all you need to do is configure the CTRIO output as you have stated (Pulse/Direction) and create a Dynamic Positioning Pulse Profile. Dynamic Positioning will allow you to simply put the absolute position (not the relative one) in a V-memory location, and set the Goto Position bit; the Pulse Output of the CTRIO will then move the stepper to the proper position.
You can "know" the absolute position in two ways:
- Hook an encoder from the stepper to the CTRIO input and monitor it.
- Use a System Function of the CTRIO and read the CTRIO Output count
I would also advise you to use the CTRIO IBoxes (not covered in the manual).
Summary of steps:
1. Configure CTRIO Output (Pulse/Direction).
2. Configure CTRIO Input (if you are going to use a quadrature encoder to read the position).
3. Configure Pulse Profile (Dynamic Position).
4. Configure CTRIO I/O mapping.
5. Download configuration to CTRIO.
6. In ladders, put IB-1000 (CTRIO) at top; use Help file to understand parameters.
7. Use IB-1001 (CTRLDPR) to load the Dynamic Positioning Pulse Profile.
8. Set the Enable Output bit.
9. Write the absolute position desired (signed decimal) into Parameter 3 (double word).
10. Set the Goto Position bit.
Lather. Rinse. Repeat Steps 9 & 10 as many times as you need. There is no need to relaod the table each time... that is why it is called "dynamic" positioning.
Hope this helps!