Makes and model numbers would help us help you.
If you are connecting to a PC you would connect the powered sub to the subwoofer output (orange jack). The second output of the orange jack is the center channel so that would connect to the 5.1 setup along with the green front and black rear jacks. It's usually best not to use both subs but it you want to try you would have to split the sub out and connect both the powered sub and the sub input of the 5.1 together.