I have had the same problem with my chair also but I learned that if you lay the drivers seat all the way back that ive had enough room in my car. I also put towels across my seats so the water or wd40 doesnt get all over the seats. I hope this helps you out some.

Try a different method of loading your chair.  I load my chair in what might seem a strange way, but it works for me.  The way I see most people do it is the way they taught at rehab; transfer in the car, get your feet in, put on seat belt, lean seat back, take off wheels, throw them in car, drag chair across your chest in the car, readjust car seat, go.  I did it that way for a little while, but as a C8 quad with no trunk control it put a lot of strain on my left shoulder and I would knock the rear view mirror almost all the time, and as careful as I tried to be I did get a few scratches.

I started experimenting and found a way that works better for me and is faster.  I transfer in the car, but I leave my feet out so I'm sitting on the car seat with my feet on the ground.  I take my cushion off and set it upside down on the passenger seat.  I pop the wheels off and put them in the back seat one at a time.  Then I grab the bar under the seat (I have a TiLite ZR) with my right hand and lift it up, then in one motion lean back and lift the chair over me using my left hand to stabilize it and set it in the passenger seat with the back down and the foot plate sticking up and against the back of the car seat.  Then I put my feet in and go, well I do reach over and buckle the char in with the seat belt because if I have to make a sharp turn or hit the brakes hard I don't want it moving (plus if I get in a wreck I don't want it flying around and hitting me).  I don't have to mess with the car seat or get dirt on me from dragging the chair over me.

I'm usually by myself so I normally put the chair in the passenger seat, but I can put it in the back seat if someone is riding with me.  Instead of lifting it over me and setting it in the back seat, I stop half way, turn the chair 90° and drop it in the back seat.

Getting out is just the opposite.  Before I start I reach over and set the chair up to make it easier to grab.  I put my feet out, lean back, grab the chair and lift it over me and set it on the ground with the back facing me.  The weight of the chair will pull me up.  Then I reach back and get the weels out and put them on, turn the chair around, put the cushion in and transfer over.

I think that happens to most of us!  I have been in my chair since I was 5 years old.  So when I started driving I immediately scratched the inside and driver side of the car.  I've put the soft side of velcro on my driver side to keep the paint pretty (they have grey, black and white at most hardware stores).  My friend got a hard plastic sprayed on her new car and she said it works but it kind of expensive.  It's the same product they use for the truck bedlines.  I hope this helps!