The XX Atlas adapter on a Jamma harness to play Pandora Box is all plug & play, the extra inputs (kicks) would connect to the Atlas via kick harness, in my case CPS2 kick harness.
Aero cities are wired with a jamma adapter of it's own. Other cabs do this as well and they are all proprietary. As long as you have that set up intact and in working order you should be fine. From there there are the "molex" connectors for several things. If you are missing the other end of the 2p, you might just be able to get it on ebay, or perhaps someone here has access to other sources.
You can still play Pandora box with the atlas on 1p though, no need to rewire anything. What kind of CP are you using on that cab ATM? If you don't have a CPS2 kick harness you might need to add that to the cab in order to use the 3 kick buttons. Maybe you already know about all of this, I dunno. There are diagrams for Jamma and for Pandora Box, check it out, then you'll understand what the atlas adapter is doing, just rerouting signals basically.