The Onkyo RC-649M remote was included with the Onkyo HT-S790 (with the HT-R540 receiver), among other sound systems. The directions for using this remote are thus in the HT-S790 manual. Onkyo has this manual here:
https://www.intl.onkyo.com/downloads/manuals/pdf/ht-s790_manual_e.pdf . See pages 13-17 for information on using the remote. Look at page 69 and the subsequent pages for the remote control programming directions and code list. To program the remote for a specific device, press and hold the Mode button (TV, DVD, etc) that you want to program. While holding this mode button, press and hold the Display button (the lowest button on the left side of the remote) for 3 seconds. Then enter the 4 digit code that applies for your device/manufacturer. (If there are multiple codes, you will need to test the remote and try again until you find a code that works.)
I hope this helps.
Cindy Wells