Set them all down so the SHOULDER of the arp stud is what is stopping it going in any further, if they become bottomed out then when torqued can pull the threads in the block, so check this, I needed to trim 2mm from 2 of mine, but it is totally normal for the rear studs to sit lower, about 5mm if I remember right, doesn't cause any problems.
I use a group a Yb 0611 HG, and torque to 120lbft, leave a minimum of 4 hours then retorque again at 120lbft, failure to let it "rest" for 4 hours before retorque can result in a blown gasket.
tabetha