For the past few weeks I've had my guitar in c# standard tuning to play some btbam. It's an ibanez rg with a fixed bridge and the strings on it currently are skinny tops, heavy bottoms (I was playing drop d mostly). It's held tuning quite well but sounds kind of muddy.

Next week I'm putting new pots and a new neck pickup in my guitar. What string gauge do you guys recommend? And are their any adjustments I should make to set it up better for this tuning?
I found that thicker strings plays well in drop tunings, the tension is higher than light strings so it plays better and it isn't so loose. Try some Ernie Ball Power Slinkys.
I use 12's for playin btbam and behemoth. So try those.
Quote by LuthierofTexas
You have no experience with racks??? What kind of guy are you?
I'll agree with nilpferdkoenig, 12's if you normally play 9's in standard or 13's if your nomrally play 10's in standard.

As a general rule of thumb I go up one gauge for every semitone I tune down. Now if you are going to drop that C# down to a B to play drop B tuning you may want to buy a single thicker E string.