To do this, you need to set up a straight edge along the length of the bike to provide a datum for the wheels. Tie a length of string to a spoke at the front of the front wheel and wrap is around the tire, running the string to the back.
Pull the string tight - you can wrap the string around the back of the rear wheel and tie it off on something convenient. It's very useful to have a bike with a rear stand here, because centre stands get in the way of your string.
You'll note the chopstick under the string at the front. This is there because I have a 3.50 - 19 tyre at the front and a 4.00 - 19 tyre at the rear - so the diameter difference is 0.5" and I have provided a 1/4" spacer (the chopstick) to compensate for this difference.
There is a 1/4" gap at the rear of the front tyre, due to the diameter difference to the rear tyre.
Unfortunately, I also have a gap between the string and the front half of the rear tyre. This is because the rear wheel is not aligned with the front wheel.
You can see this gap here:
Use the tool kit spanners to slacken the wheel spindle:
Use the chain adjusters to move the spindle forwards or backwards. Since my chain tension is correct, I don't want to move the nearside of the rear wheel - I will correct the alignment by pushing the offside forwards.
Now, the front and rear edges of the rear tyre touch the string. I'll check the front wheel has not moved and the string is straight:
Tighten up the wheel spindles and the lock nuts on the chain adjusters and you are done.