It seems a stupidly obvious question but it turns out to have several different answers.
If you want to know where to place the bridge saddles, you need to figure in compensation. If you want to know the proper heel to bridge distance or anything else involving the uncompensated length (ie what is the actual scale length) then measuring from the nut to the twelth fret and multiplying by two is what you want to do. If you want to know where to drill holes to put your adjustable compensated bridge, you need to measure the nut to twelth fret, multiply by two, and then make sure that the thinnest string at its forward most setting can reach that position.