Check your polarity first....
Adam,
Since nothing else changed (so it sounds) that all you did was try your Aux circuits then go direct to the Batt. (Don't know why the aux circuits are dead, puzzling) Check and make sure that you didn't cross the Pos and Neg. feed to the breakers when you reconnected the panel. If that is not the case then since all other circuits trip, you managed to create a short some how (assuming it all worked before). It may sound complicated, but it looks like you did minimum invasion, shouldn't be too hard to figure out. The key to finding the problem is going to be SLOWLY and METHODICALLY starting at the battery and going to the circuit panel. Use a circuit tester (multimeter preferably) and check polarity and voltage. The panel circuit should be Positive (everything that feeds the breakers / fuses). I am not sure how your boat is wired (OEM or did a PO change it). But for starters, positive from battery feeds the breakers / fuses. These feed all your circuits and then the negative connect all together and go to the battery negative. How handy are you electrically / mechanically? In replies we can get overly simple or overly complex. If you don't know this group will work you through it. Afterall, you can't call an electrician in the middle of a lake.
Nik