How do you program a stepper with an encoder for feedback?

I have a DL06 PLC,HO-CTRIO Counter Module,STP-DRV-4035 Stepper Driver,TRDSH 100BD Encoder, and a Stepper I already had.
Done all of the wiring and all works well with the CTRIO Workbench Programs.
I have been able to use some of examples to move the stepper motor and read the counts of the Encoder.
My problem is trying to put both the stepper moving part of the program with the Encoder reading part of the program.
Can anybody help me?

Steppers are so called "open loop systems" and do not require encoder feedback for functionality.
Optionally, encoder reading may be used for motion monitoring, but it does not have to participate in the stepper motion control.

I quite often use a stepper driver and encoder. All I do is let the plc output the pulses to the stepper drive, and when it is finished, I check the position with the encoder. If it is out of position then I flag an alarm. I don't use the encoder until the and motion has stopped.
All you have to do is tie up the encoder counts to the pulse outputs and compare. Generally this works without any problem.

Easy: Use a Berger-Lahr TLCC system with a CANbus-encoder equipped stepper motor, and the pre-built and supplied closed loop software routines.

Nothing beats buying the right hardware and software for the job!

Nothing's more difficult than trying to make something unsuitable for the job...suitable.

Good luck.