Bongos gave me a lot of trouble with Stances, but i finally figured out what makes it tick.
Basically, bongos designates certain bars for certain stances. For example, if you have 8 action bars, you can designate it so bar 6, 7, and 8 represent battle, defensive and berserker stance.
This is currently what i have set up right now. When I switch into defensive stance, Bongos will shift Action bar 1 with Action bar 7; when in battle stance, action bar 1 with action bar 6, etc.
To accomplish this, right click on action bar 1, and go to stances. You should see several slider bars, 3 of them labeled "Battle", "Defensive", and "Berserker". Now, say you have 8 bars, and you want Bongos to replace action bar 1 with action bar 8 when you switch into Berserker. Simply drag the slider until it says 7, meaning action bar 1 will jump 7 spots to action bar 8 when switching stances to berserker.
Then, you can drag your abilities for berserker mode into action bar 8. Once you are finished, go to the visibility options for Bongos, and turn off action bar 8, so that it effectively becomes invisible until you switch into Berserker stance, in which case it will show up where action bar 1 is.
Repeat this for your remaining stances, keeping in mind that you must drag the sliders in the Stances menu of action bar 1 to designate which bars are replaced. So if you drag the Battle Stance slider to the number 4, Bongos will switch action bar 1 with action bar 5 when switching into battle stance, etc.
Hope this helps, it literally took me hours of toying around and experimenting to figure it out, the guides online did not help at all.