Mixing up the cables can melt the jump cables and the batterers thats about it. Sounds like you have a bad battery or you have a lot of resistance in your battery cables. Do you have a lot of the green shit on your positive terminal? An alternator only charges the battery it can cause a no start but normally your battery light will come on the night before if your alternator is bad. If you blew your main fuse you would have no power in the car at all.