Well, there are some uncertainties.  First, we don't know 100% which IR protocol your STB uses. I don't know for sure about the remote you linked, which has motion control built in, but its sibling remote can handle both 1.253 and 2.253.  It has the Cable 1631 and TV 1523 codes built in. If your STB uses 2.253, we'll need to use the 994 command (shown in the Extended Instructions) to manually assign the functions, since this setup code is intended for a TV instead of a STB. 
But assuming that your STB uses one of the two above IR protocols, we'll be able to make it work.

Your Onkyo Receiver can use any of Audio 1320, 1805, or 1993.