You can't mix the SUP1A with the SUP2 in the same chassis. So the answer is no to put the SUP2 into the chassis with SUP1A for preparation of the config. It is quite possible that you can cause a spanning tree loop with native VLAN mismatch if you decide to work on the config of the SUP2 in a production environment. And there isn't any way of configuring the SUP without the chassis. Here are your only 2 options I can think of:
1) get a spare chassis and power and pre-configure the SUP2
2) pull out all the modules and disconnect all uplink when you are inserting the new SUP2, get the configuration into the switch and re-insert the other modules (this can get very complicated to avoid issue).
HTH,
jerry