There is a 'help_doc' on sf.net. Check the link in my signature.
You changed your controls because you typed the 'Short-Cut'. You can disable some of them. Look into the 'nesDS.ini' for more information.
----nesDS.ini-----
;B_A_Swap
;KEY_START | KEY_LEFT
swapab=KEY_START | KEY_LEFT
----nesDS.ini-----
change them to
----nesDS.ini-----
;B_A_Swap
;KEY_START | KEY_LEFT
;0 to disable it
swapab=0
----nesDS.ini-----
All the short-cuts can be disabled if you don't play a FDS game.