Mechanical Caliper/Disc Setup

[boolay]

I have Shimano BR-M465 Calipers and standard discs on my Kona. I have just replaced the pads front and back, and when I fixed the calipers back to the frame and adjusted, I was struggling to get a happy medium between pads not rubbing and having effective braking.

I noticed I was also getting a lot of sideways movement on the rotors (warped), so I have ordered some replacements to help solve the problem.

Is there a correct method / series of operation to setup a mechanical caliper?