Windows will not go up or down

[xlr8cj 0]

I recently replaced my passenger window motor because it broke. After putting door back together and window working for day or so I went to buy a new battery. I have always had a power drain where my car wouldn't start after sitting for few days. I came out to my car the next day and both of my windows were down and wouldn't go back up. I here clicking in the door motors and in the back area coming from the electric window module when i try the windows. I have no idea whats going on. At first I thought I could have blown a fuse from having a short or bare wire because I have an after market stereo system also and the fuse repeatedly blows when I try to replace it. I don't wanna replace the module if it may not be the problem. Can anyone help me at all? Another question, where can I find a fuse box diagram? The previous owner did not have it so I'm going at this blind.