To align the brake shoes on a caliper that carries the orbital mount for the shoe holder, here is a little procedure i have found that works for myself.
Firstly tighten the brake shoe holder in the caliper arm just enough to allow some movement if you push on it with your hand.
Then apply the brakes lightly and manually adjust with your hand, each side of the lighly tightened holders so they now align themselves evenly to the area of the rims brake surface.
Now apply the brakes again firmly this time, this is to allow the shoes to seat themselves level to the rims surface, while checking visually that they stay even in relation to the arc of the rim by the tyre, adjust them manually again if they aren't quite aligned yet.
Once you have got the set up correct, you can now tighten them a little further to snug up some more of the freeplay in the holders.
Finally you place a 2.5mm allen key at the rearward facing part of each of the shoes, letting the angle part of the key sit above the shoe on each side so it cant slip down, and press the brakes firmly again, this last procedure with the keys in place allows you to set the toe in angle of the shoes.
If you did it with a little patience, the shoes should now be positioned correctly, and all thats left is to give each shoe holder their final hand tightening, taking care not to move it around; the brake shoes alignment and toe in should now be set correctly.