It doesn't matter nearly as much as you'd think. The main difference is for CB, where you're going to want to take either Giantslayer or Warmaster, which is largely useless outside of CB.

Since neither Visix nor Kymar will be used in CB, you should have no problems with their masteries. Kymar will want to go Red / Blue, and Visix will either want to go Red / Blue if you're mainly using her for the TM control on her A1, or Red / Green if you're using her as a provoker and damager.

You *could* go Green / Blue for Visix as a wave controller, but given her kit, I think you'd be better off with Red / Green. For dungeons you don't need a whole lot of accuracy, and the TM boosting blue masteries aren't really that important for wave control.

That said - I don't use Visix, and Kymar for me is built exclusively for arena, so take this advice with a grain of salt.