You can just use MultiUpdate to upgrade, it will not touch configuration.
Also in Help menu there is a backup/restore that will backup/restore configuration
Or from with in MC type ":goconfig" in the commandline field, it will take you to where your personal config file are located.
For portable they are stored in the Config folder (history info in SessionConfig folder, it is like last info search for, and last entered info, and such, stuff that get autofilled based on what you did before)