Not to be snide, but so far you have told us your quasi-generic PLC isn't working like you want it to.
We don't know which model you have.
We don't know which mode you are trying to configure.
We don't know how it is wired.
We don't know how many channels your encoder has and how they are wired.
We know you have at least one encoder channel switching at 12VDC levels.
We know you don't see X0 status changing somewhere.
You really are going to have to help us help you.
Lastly, this is a forum for the CTRIO cards which are not what you are trying to use at all, but that is not as important as the other things.