Booking Manager allows you to enter any number of payments methods as described in How to enter payment methods article.
However you may want to temporary deactivate some without deleting them or you may want to change the default payment method.
How to activate/deactivate payment methods
Open Preferences > Reservation settings > Payment methods (1.). In there you have list of Available payment methods (2.) entered in Payment method editor and list of Selected payment methods that can be applied to reservations.
To make a payment method available, select one from Available payment methods, click on the arrow (2.) to move it to selected and press Apply (3.).
To remove a payment method, select one from Selected payment methods, click on the arrow (2.) to move it to available methods and press Apply (3.).
How to change the default payment method
The default payment method used on newly opened reservations is the first one (1.) in the Selected payment list. To change the default, select the one you want make the default (2.), click on the up arrow (3.) to get it to the first place of the list and press Apply (4.).