Log out your characters, and while at the character selection screen, select the new ISBoxer Character Set from the IS menu like you're launching it. It will switch teams for you and reload its settings (similar to hitting Export) automatically.

Things that do not change when switching teams like this:
* Window Layouts
* Action Target Groups (they don't clear out automatically, this will get fixed in a near-future update)

Closing out and restarting remains the cleanest way of switching teams. This new method of switching was mostly added to ISBoxer 34 for people with authenticators that now take a couple minutes just to log in.