Sounds like your house is set up right to me.
answers to your questions.
1. Mine does the same thing, most of the time I don't even use the bar that goes in the back.
2. First thing I do is drill my holes and clear the snow, then I just start flipping it up and pulling the bars out till they snap, turn the heat on and fish. I don't use it as a wind break but I think that is what that back bar is for. Put that in and just let all of the others rest against it.
3. Yes alot of the fabric is on the seats when it is folded down, I never worry about the seats pinching, Just make sure the seats are down before you close it then the fabric will be on top of the seats. You can also slide the seats forward so not much fabric is on them. Also I have found that it is best to have the door closed when it is folded down.
4. Don't have any pics but I normally put my buddy heater in one of the corners, A bucket between the seats along with my vexilar and camera, and my rods go in the opposite corner on the floor right along the chair supports.
It takes some time to figure what is the best way to load it but you will get it. Practice at home before you go to the lake and you will get the hang of it.