It depends upon your wiring. The general rule of thumb is that the higher the pot resistance, the brighter the tone. That said, humbuckers are usually done up with 500k pots and single coils with 250k.
If you have a 1v 2t setup, then you could consider a 500k for the v and the humbucker t, and then a 250k for the single coil t. If it is a 1v 1t setup, I'd use 500k all the way around.
Experiment and see what you like. That is the best advice I can offer.
This will likely confuse you even further: what about tone caps? 0.047 uf are usually recommended for single coils and 0.022 uf for the humbuckers.