Scroll to the last page of this document for the wiring diagram you'll need:
With current EMGs you have to use their provided electronics, and "Quick Connect" system.
In order to do this, you will have to enlarge the pot holes, and possibly the routing between your pickup cavities and the control cavity.
EMGs provided pots are mini pots, so they leave a fair bit of room behind them in the control cavity, which leaves lots of room for the battery. The problem you'll likely encounter is the Battery buss, as it's larger then the battery, and really doesn't fit anywhere, so you may have to do some routing within the cavity to make it fit.
The reason that the battery buss is needed is that EMG offers nothing in the way of toggle switches (though they do have "Quick Connect" Fender style switches available). So, you'll have to provide your own toggle switch, and solder the wires onto the switch, and then at the other end of these wires, they go into the little set screw clamps on the battery buss.
EMGs are a bit of a pain in the a$s, and before you take the plunge you may want to look into other options, and be totally sure they're the only thing that can work for you.
Seymour Duncan Blackouts or Livewires could be good active alternatives. Gibson, DiMarzio, Seymour Duncan, all make good passive alternatives, at lower prices than a set of EMGs. If you want to stick with the EMG price range though, you could look into Lace, who make a load of alternatives that will likely sound much better than EMGs, or some other boutique manufacturers.