They can not make you check your CPAP machine. It is a medical assistance device under the ACAA. It sounds like you carry it in a bag which includes others items so they can make you check the bag, but not the CPAP.

It doesn't matter on which side of the cabin you sit. All of the overhead bins in your cabin are first come, first served so you can put your bag in the opposite side if necessary.

If the bag is a "legal" carry-on then it will fit in the overhead bins. With the old bins it fits long-ways, with the new ones it first wheels first. It is only in FC that the bins on the left side are too small for a rollaboard.