I also store my bike in the trunk of my car w/ both wheels removed. Here's how I reinstall the wheels w/o putting the drive chain into the dirt:
-take both wheels out of the car and lean them against the bumper so that I can reach them (i usually put the wheels on top of the frame in the trunk-- cover the frame with a blanket so no scratching during transit)
-remove bike frame and hold it above the ground (don't put the drive train/derailleurs on the ground). I hold the bike with my left hand and sort of brace it under my arm. The rear of the bike is in front of me and the fork is behind me (drive train to the outside, not pressing against my leg) It's OK to put the front fork on the ground and I do this sometimes to help balance it
-grab rear wheel and pop it onto the bike. This is much easier if you have the chain in the smallest cog before you remove the wheel, and if you routinely do this, you know where to thread the chain when you put the wheel back. also, make sure your brakes are released before removing/installing the wheels
-install front wheel.
It also works to put the frame upside down, though I personally have a much easier time getting the rear wheel on when the bike is upright and I am holding it.



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