No, you only get miles for one program, but you get to choose which one. You can give them your Skymiles number or your Onepass number. It's a good idea to check at the gate, make sure the correct number is in the system.

There are elaborate games that can be played with booking with one number and switching to the other at the gate; those are done, for example, to play with the upgrade lottery (airlines will upgrade their own fliers first) and then switch to book miles on the other airline. However, when it is all over, you only get the miles on the last one you present.

Always save your boarding passes, if you don't get credited with the miles you can fax those in as proof.