I dont know if this is the right way or the wrong way but i initially set up so it looks centered.
Then with the bolts just done up but not nipped tight, I use the bottom of a small pin hammer to gently tap one side or the other to bring it till the point the rotor doesnt deflect when i pull lightly on the lever.
I sight straight down, pull the lever that little bit till the pads engage, if the rotor is starting to deflect one way, i use the base of the hammer to tap it lightly then try on the lever again. Its a case of a bit back and forth to get the caliper to a point when i pull the lever the pads press onto the rotor and the rotor doesnt move.
By using a small pin hammer, it has a bit of weight behind it so you can have the bolts reasonably done up, but not so that they are too loose, and when you do come to tighten them the caliper doesnt move by twisting as the forces on the bolt to caliper make it do.
Because im using the bottom of the handle, the handle is quite long so it can be poked through the wheel to tap the inboard side of the caliper