It should be covered in the factory manual and if you don't have one yet, it would be a good investment for about $58. You'll be glad you got it.
You align it by using the marker hole pictured below (tan dot foward of the axle nut ) which should be on your swing arm and loosening the rear axle nut to align the wheel using a piece of coat hanger bent into an "L" shape and measuring equal distance to the center of the axle on both sides. Then retorque the axle nut to specs. and reinstall a new cotter key.
Some bikes do not have the alignment holes and the pivot shaft for the swing arm can be used then.
There's always the straight edge to the front wheel and across the rear wheel to double check your adjustments.
Also don't forget to check your belt tension when you are done before locking up the rear axle.