I'm going to Montreal with some friends at the end of July and I booked the hotel was on points and miles. I was able to get two of the nights with Marriott points, and then I booked the other two nights with BA Avios. I assume there won't be any problems, should I call them prior so that they should combine the two stays? or is that something that will be taken care of at check-in/not an issue

It will be taken care of at check in, no need to call.

i have two reservations like that this upcoming week, i called ahead and the front desk agent told me they will put a note that i have another reservation for the following day and to keep me in the same room.

Different properties will pre-assign their rooms at different times. Some block the actual rooms to specific reservations and others will just deal with categories leaving the actual room assignment to the FDC. And let's not forget the picky guest that requests a specific room for whatever reason.

If you're talking about two one-night reservations, then calling or emailing the property ahead of time is wise and make sure you confirm upon check-in. If you've got a day or two before the next rez then they should be able to handle that at check-in. Also make sure you request they code your key for the entire stay so you don't have to get a new key when switching reservations (I've found many FDCs don't know how to do this).

Of course, this will only work if you booked exactly the same room category/type.