You should be using memtest86+, but, anyway, yes, it checks all the RAM that is installed. (Well, all but a few hundred K needed for the program.)
You always want to check with all the DIMM slots populated, just like how you normally will be using the computer, with all of them in there.
You also want to make sure you have at least 4 full passes, since some machines are really slow at testing, overnight might not give you more than 1 pass.