The boards identify themselves to the mother board. Plugging them in is a matter of convenience. Usually there is a small right angle bracket to hold the opposite end of the BMDC to the back of the electrical enclosure.
Is the CMOS battery a Dallas real time clock? In other words a IC type? Or is it a Nicad type made of 3 cells welded together with heat shrink around it? If the Nicad type, it needs to be unsoldered as it will eventually leak and destroy the mother board. If you use an external battery, they typically come with a plug to plug into the mother board and a jumper is moved from internal to external battery.
The only landmine is that the older BMDC did not have a shroud around the ribbon connector in the center of the board. If this ribbon cable is plugged in wrong, it will smoke and melt.
George
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)