I'm scared to drop too much $$ on car upgrades etc- seems a common bug where cars are disappearing from not only the garage @ the homes of the characters but also the outside garages... saving them @ a garage, saving game, coming back and car is gone- not at impound or garage. hope they patch that soon. Also sounds like taking a car on a mission can cause it to disappear as well.
Basically what I did is this...you get a car to begin with that respawns. Take that for missions unless you need a fast car then use the Adder which is easily relocated but don't upgrade it. Save your upgraded cars in the garage for races and to cruise around. The good thing is the races don't restrict your car.
Garages are easy to use. Just drive up to the door and you are prompted to press right on the d-pad. Do that and you will park the car inside. Then just walk to the door to exit and your car will remain there. Quicksave via the phone and you're done. To retrieve a car simply walk to the garage door and press right on the d-pad to enter. Then get in a vehicle and you will be placed outside. I have never had a car disappear from the garage. If you crash it, die, or get arrested you will lose whatever vehicle you were driving at the time. So remember not to use your upgraded cars for missions and the like. Though after missions, go to the impound. Your car will be there but it will cost $250 to get back. This is why I keep two adders in my garage. One has all the upgrades on it and the other is stock. I can take the stock one out if I need to and I keep the good one for races. You can store cars at your safehouse too by simply driving in and getting out. The car will stay there until you take it. The outside garages can store multiple vehicles. You can also store bikes, I have an upgraded Bati 801 in one garage too.
Also I don't know how but I got an Elegy RH8 that I can access from my garage with Franklin at any time (I was prompted to press the d-pad right to access special vehicles inside the garage), also an assault SMG for free with all the upgrades from Ammunation. I did not buy these and I don't remember finding them. Anyone know where those came from? The only stuff I unlocked that I remember was from the ammunation shooting range challenges. I got an AP Pistol for free that way. The SMG and assault rifle I had to buy from the store. I also entered the blimp code but it didn't mention getting anything else from that.
Oh and don't load the game from an autosave, it will put you at your safehouse and you will lose the car you were driving if you were driving one when it saved. That might be what is happening when people say they lose cars. if you don't park it or load from a quick save, you will definitely lose whatever you're driving.