Don't forget that the number in each command zone is how many deployment points you will receive for controlling it every 4 seconds. The most valuable command zones tend to be where the most conflict will happen. So, if you find yourself taking and spending a lot of points to defend a low point zone, you might end up paying more to hold it than it will ever give back to you. Keep that in mind when choosing which command zones to take.
Personally, I tend to leave command zones around me, and advance quickly to the command zones I feel will set me up with a good base of operations for advancing or defending. For instance, on the map "Dual Fields," as NATO, I immediately rush toward the command zone closes to me in the central village. Controlling this, I'm able to set up a strong defensive position and control the middle of the map. The command zones behind me, closer to my start zone, I will dispatch command vehicles to when I feel I need to, later on. This might be because I find myself unable to adequately create the force I need to counter the enemy without more deployment points, etc. A good thing to do is zoom out to satellite view and calculate how many command points your enemy will be getting total every 4 seconds, and how many you will be getting. I don't like the enemy receiving more income than me.
As for control point protection, I am not at a high enough level yet, and don't play against a high enough level, to need to put too much thought into command zone protection. I usually move my first FOB and command vehicle back to a better area of my first zone, and always place 2-3 cheap AA units nearby it to protect from hunting choppers. Also, I have begun, as I have improved, to place a few cheap infantry vehicles nearby it, too, to protect from infantry drops. When I secure a new zone, the first thing I do is buy 2-3 cheap AA to go with it in order to protect it from marauding choppers. The worst thing is saving enough points to buy an expensive command vehicle only to have it immediately destroyed once the enemy gets the alert that you've secured it, and he/she dispatches helicopters to it, hoping for an easy kill.
See me on W:EE as TheMightyCthulhu.