If you want to make the battery pack 'external' like that you'll have to desolder the AA and PnC battery pack connectors form the controller board so you can mount them to the back of the controller shell.
You'll need to remove the connectors, then solder the length of wire you need to them, don't solder the wires up to the controller just yet or you'll have that whole mess dangling from them while you're trying to glue them to the shell.
After that you'll need to glue the terminals to the shell in the positions they would be in normally. All that's really needed for this is hot glue, but if you're looking for it to be permanent to the point of needing a Dremel to replace the terminals if you ever have to, then get some Plastic Welder by Devcon, there are other 'plastic epoxies', but if you want a good one that Devcon is it, but hot glue will do the trick as well.
With the PnC connector you'll want to plug a PnC battery pack in the shell so you have that as a spacer and guide so when you hold the connector on there it's in the exact spot. Hold the connector there, make sure you have it oriented the right way and put a bit of hot glue on each side and then hold it in place until it's dried, give it a good couple minutes, then take the battery pack out (while still holding, not pushing, on to the connector) and you should have it there all lined up. If it's not perfect don't worry about it, it doesn't have to be. After that go around the connector with a good bit more hot glue to hold it in place. *(If you're using plastic welder instead, you'll go thru the same process up to this point, and it's best to use hot glue first to hold the connector in place, unless you plan to hold the thing there until that stuff cures, 5-10 minutes, either way it all gets done the same)
Pics of how some of the process typically goes..