Storing your Car
If you are storing your car for the Winter (if you are in an area that has bad seasons), it is better to put the car up onto jack stands. There are quite a few reasons to do this. First, it makes it alot easier to work on and under the car all Winter long. Second, it helps air flow underneath the car. If you have a concrete floor, sometimes moisture seeps up through the concrete, so it is better to have it higher off the ground to create better air flow under the car. Third, it keeps the tires off the ground so flat spots don't develop on the tires and also to keep the tires away from the moisture as mentioned before. When you place the car up on jack stands, use the recommended locations for placement of the jack stands. The jack stands should be located on the frame and axles of the car (see below). Also, you must make sure that you have the car evenly supported and level. A good way to check this is the doors, hood, and truck should open and close just as easy as if it were sitting on all 4 tires. If you have a hard time closing and opening the doors, then you don't have it sitting right and you should take it down and do it again.
Things you should do
The second thing that you should do is disconnect the negative battery cable. Once again there are a few reasons for this. First, it saves the battery from being drained by the car (clock, etc.). Second, once again, it makes it easier to work on the car. If you are doing any kind of electrical work, the battery should be disconnected for this so why not do it now. Now if you are storing your car in a non0heated storage space (somewhere where the tempurature drops below 35 degrees), then you should disconnect the battery and take it home with you. If you keep your battery in very cold tempuratures it will go bad. Like I mentioned with air flow above, you also want to have your windows open a crack to allow air into the interior of the car. If you keep it closed up, it will start to get moisture build up and get that musty smell to it, so just crank both of the windows down just an inch or two. Another thing you should do is put in some fuel additive so that condensation doesn't build up in the gas tank. Now I knew that I was going to be storing my car and working on it all Winter so I installed a gas heater in my garage and keep the temperature around 62°. If your garage or storage facility is heated, then you don't need to put the additive in the gas tank.
Another thing to watch out for is covering your car. You need to make sure that you have a soft car cover so that it doesn't cause any scratches. But there is more to watch out for. Even if you do have a soft car cover, you can still get rub marks on your car. Not scratches, but rub marks for taking on and off the car cover. I noticed this and had to do some touch up paint to the parts that had wear marks on them. You need to be very careful and remove the car cover with care so as not to cause this.