I can't can't get the dot to line up in my sight picture. So… ?

Sig M-17

Not quite sure I understand your question. Are you trying to co-witness the dot with the iron sights? That will get you close to being zeroed, but you need to zero the dot independent of irons. You also don't want to use (or look at) the irons when running a red dot. It defeats the advantages of a RDS (like maintaining a hard target focus and nothing to align).

I can't remember for sure on the M17, but I seem to think the rear sight comes off when you remove the cover plate to mount the optic. That's how one of my P320s worked. On a different 320, the rear sight stays in place, but because the DPP has a very thick housing, you can't co-witness with the standard factory sights (they sit too low).