Someone said it is the BCM

Changing the door actuator in my truck that I have gotten out of a junk yard. it was not the exact same match but the same wire colors. in the process of cutting the wires and attaching them I shorted out the big orange wire which I thought was hot, I guess it was not. anyway assured the wires out and now my windows and radio do not work. I checked all fuses tried everything. also, to start my truck now I have to turn the key to the on position to get out put the fuse in attach the battery cable get back in the truck turn the key to the off position and it cranks. then I turn the key on position and drive when I get out to shut it off and pull the battery cable off. someone said it is the BCM. I have a new one coming. I wonder how I get it programmed? I have no idea. do I have to go to a dealer? there are so many issues here. someone help please.