New install mixed up my MS FBB stick settings with my CH pedal settings...can I reverse this

[Blitzen]

First time I ran the new re-install of GB I got a screen I have never seen before saying something like "...have detected a new control device ," and giving me a few options one of which I had to check in order to proceed further.Well even tho the pedals aren't new it was the only option that made any sort of sense...I guess, but no now in game it screwed up my key settings tied to the joystick royally . They were changed in some way to make me have to re-set all of them & now they had whole new placement titles & some don't seem to work at all. So two questions : 1.) what should I have chosen ( in case this option happens again down the road?) 2.) How can I get the joystick settings to work again as they have in the past?

Thanks!