You can't align the rear axle. Once it's in, it's in. As for the fronts, I've always just eye-balled them.
to check your "front" toe allignment
tie a string around your entire quad (yarn works fine) and adjust your tie rods so that the back of the front wheel (sounds confusing think about it for a second) is BARLEY touching the string. Then adjust the tie-rod so that your about .25in toed in. To measure the toe just measure the distance from the front of the two front tires. it should be about .25in LESS than the rear of the front two tires.
Make sure some one is holding your handle bars str8 white you are making the adjustments, or if your alone strap it to the grab bar real tight so it does not move.[/b]