Anyone know anything about disc brakes?

New wheel in, undo calliper bolts, apply brake, tighten bolts

What brand is the centerlock hub? If it is shimano with a 10mm axle, some locknuts are thinner than others. Change left locknut to one 1mm thinner and add 1mm spacer on right side (and optional re-dish wheel slightly)

or fiddle around with different spacers (part 6 and 3):

You were unlucky enough to ask that question just after the previous couple of pages had been used to answer it :)

in order of preference if not practicality...

• get rid of the six bolt wheelset and use the same hubs on everything
  
• respace the CL hubs, if you can, as above
  
• use six bolt on your CL hubs via an adapter, and then shim them in to the same plane
  
• fiddle with the brakes each time you move between 6 bolt and CL
  
• shim the centrelock rotor outboard with something - might damage rotor, hub, face.
  

The answer is use the same hubs and rotors. Centrelock shims are a bad idea and resetting the brake calipers is effert (although less so if you have hydraulic).
This is also lfgss so the actual correct answer is buy more bikes for your multiple wheelsets