Ill tell you very quick how the vac2 disabler works:
It gives you a cracked Steam.exe file, when you use that Steam will open as usual, but when youre playing MW2 it will stop the VAC protection, which means you can hack, so as soon as you dont EXIT the cracked steam.exe it stays that way (No VAC in MW2) but if you Exit and open the old and real steam.exe then the protection will come back on.
Its pretty simple said this way, and you can also make a cool little feature which opens your cracked steam.exe when you start up windows / mac(phail) / linux(phail) instead of the normal one.
So remember, always check if its the cracked steam.exe your using after shutting down windows.
Edit: Uber short version ;b
NO you dont have to do it all over again, only when you turn off, restart your computer or whatever, to be sure