Q: Charging system failure.

ok so I just replaced my alternator and in the process blew my alt fuse I replaced that and I still had a battery sign on I'm running 2 optima betties and a normal battery under the hood. as soon as I pulled in to work my dash lights went out and the radio went off everything else was good headlight and dome lights were good the truck stayed started then I turned the truck off and it wont start no clicking or anything the door sign work on the dash and that's it dome lights work headlights still work but no start now I have a single 15 that was killing my alt so I unhooked it as soon as this happened what should I look at next to see why its not starting also none of the windows will go up and b4 this happened some time when I use my signal light the head lights go out

My car has 280000 miles.
My car has an automatic transmission.