It doesn't look like you actually need to care where the battery is, unless it's already dead. The instructions explain that the backup battery will be activated if power is removed from the OnStar module while the ignition is on or RAP is on. The backup battery is intended to allow OnStar to continue to work if power is lost when the car is "running", like if you crash and the 12V main battery gets disconnected. As long as the ignition is off and RAP is off (which happens as soon as you open the door after turning off the ignition), you can disconnect the OnStar module without regard to the back up battery. It won't be activated and so, will be as good after the OnStar upgrade as it was before the upgrade.
Also, the comments and image in the instructions you linked to above imply the backup battery is plugged in to the back of the module per the red circled "1" on pages 11-12 (which, BTW, is logically the best place for it since it ensures the module gets power in a wreck unless that section of the car is destroyed).
I would note that it also appears you need to reprogram the new module after installation and you'll be needing a Tech-II for that.
And lastly, depending on how you want to read the preamble, it looks to me like successfully replacing the module is only half the task. GM may only be providing the back-end OnStar support for vehicles it knows have been officially upgraded. You go through all the trouble of replacing your module and it might not get you anywhere unless GM is willing to "relist" your vehicle for the service which I'm betting is possible but will be like pulling teeth.
