We change the model to accomodate the tolerance if it is bi-lateral. I think you would have to do the same.
I would recommend that you just leave your model at nominal. The Mastercam programmer will just use "Stock to leave" if need be. Tooling like carbide endmills comes standard +0/-.003 so the CNC Operator is use to have to tweak things to make it within tolerance anyways.
I would ask your CNC machinist/programmer what they prefer. In our shop they want modelded to nominal. +/-.002