Hi Xavi,
It would have been better to post this under the DSPMC section.
That said, Do you have a wiring diagram for the omron servo driver?
There are at least 2 ways to run the encoder inputs. You could run them directly to the DSPMC and run the drive without encoder input. Tis is called torque mode. This is only possible if the drive is capable of this. If the drive must have encoder input, you must split the signal and connect it to the DSPMC as that is how it does the positioning. This of course goes back to the first question, do you have a manual for the drives?
Mike