The Quick Setup Wizard will not -- ever -- overwrite any of your settings, you can run them independently of each other in the same profile. In fact, for LOTRO it will even use differently named key maps from WoW -- Always On, Non-combat, and Combat as opposed to Control, General and FTL DPS Keys

It is very much intended for you to be able to use the Quick Setup Wizard as many times as you need in the same profile without destroying any of your configuration.

Alternatively, you can use File, Save As and keep completely separate profiles. Some people do this (I am guilty as well, my EVE config file is separate from my massive WoW file). You would just load the one you want, and Export it.