Introduction

To align the rear wheels, you will need multiple trips to an alignment shop to have the changes checked. But an alignment shop will typically charge $60+ for each report and you will need 3-5 visits, potentially $180-300. The right answer is to buy a "lifetime" alignment, typically $140. Not to worry, you can use it every time the tires are rotated to make sure things are still OK.

You will also need a set of metric sockets; an accurate torque wrench; and a floor stand jack ... NEVER WORK UNDER THE LIFT JACK. These can be found at Harbor Freight or other discount tool places. Just remember, you health and life is at risk so spend the money for the right tools.

Initial Survey

Get an initial alignment reading and look at the rear wheel values. The Prius has a 'floating' rear axle that is supposed to self-adjust. Identify the wheel with the worse toe. This is what we'll fix first:
DO NOT STACK SHIMS!
ALWAYS USE IN SAME-SIZE, SHIM PAIRS!
TOE USES ONLY THE FRONT OR REAR BOLTS!

Try not to repeat my mistake of correcting positive toe by putting a large, 1/32 shim on the rear bolts:

I started out, the upper left, with 0.30 degrees of positive toe. I put a 1/32 shim on the wrong bolts, the rear ones, and drove the toe to 0.90 degrees! But when I put the 1/64 shim on the front bolts, taking off the 1/32 shims, it came in at a very nice, under 0.10 degrees.

You'll notice the camber changed as the toe was corrected. This happens because the bolts are slightly rotated so there is a toe-camber relationship. Of the two, getting the toe right is the most important since this causes a scrubbing action on the tires. Once the toe is corrected, adjust the camber on the opposite wheel:

If the camber isn't enough, repeat the process and use a larger pair of shims. Always use a pair of identical sized shims so the opposite bolts will be torqued correctly. If you have mismatched shims, you will have a rocking motion and that can over-stress and fail a bolt.

Preventing Rust in Gap

The pairs of shims will leave a small gap between the hub and the axle with the largest gap on the side with the shims on the bolts. If you live in an area with a lot of salt in the winter or near salt water, you may want to put a layer of paint over the gap or at the gap. This will minimize exposure to oxygen and water to slow formation of rust. The bolts are treated and should be OK but the base of the hub is bare metal and the axle plate is painted. In practice, after two years, there was no significant debris in the gap and no significant rust. But I live in an area that seldom uses salt in the winter.

There is a more sophisticated alignment system, the "EZ SHIM" but early tests have been disappointing. I don't trust their instructions and my updated procedure is still a 'work in progress.' In theory, the "EZ SHIM" handles all four bolt offsets and eliminates the gap left by the shims.