search the macros forum for a post regarding synchronizeSettings in config.wtf, there are 3-4 variables that let you turn WoW back to the mode where it stores all macros, keybindings, etc on the client machine. I've done that and have seperate wow dirs for multibox mode and single player mode.

There is also a mod called ActionBarSaver that lets you save wow (and other mods that use default wow button configs, like bartender4) action bars into sets and swap with a command. So I have a resto solo, resto multibox, ele solo, ele multibox, and PVP button set on one of my shamans for example. I think you can do this inside Macaroon itself, including swapping keybindings, so you may want to look into just using Macaroon by itself.