Not sure what you mean with that, guessing you mean difference between the onboard and custom? The custom ones are much more efficient than powering the wii with the official ones, since the official ones are built to be cheap, and custom regulators are built to be efficient (thus longer battery life).
If you mean the difference between trimming a board and using custom regs, and not trimming but still using custom regs, the only difference is that you will have to remove the onboard regulators before you hook up the custom regs so you don't have issues.