I guess you can do it that way, but make sure to delete all the stuff that is in autoexec.cfg when you do that. I am unsure if addfile works in autoexec, you could use batch files, or the launcher to add wads.
Sometimes, when certain wads are loaded, it won't execute autoexec.cfg right away, or at all. If you run into one of those, just type EXEC AUTOEXEC.CFG in the console, and your autoexec will be loaded.