The account and subaccount thing, should eventually go away.
You'll want to use the option to virtualize the config.wtf for each toon you play.
So each can save their own settings, for the next time that toon is played.

If your character set assumes Account A is in Slot 1, if you log on Account 2 in that slot, you'll get an error (with IS Boxer wanting to update stuff for you, when you export to IS).
Once you log on, with the correct account in the correct slot, IS Boxer will be happier.