If you've got a wind trainer then you should use it to get the alignment sorted. Here's how i managed to sort out my cleats:

Start by wearing what you normally wear: sox, nicks, whatever
Make sure your bike is level. Chock up the front wheel with wood, books, whatever
Loosen you cleat on one shoe, then nip it up so it can be moved with your foot, but will hold its place.
Warm up for about 10 mins, concentrating on your pedalling action. Smooth and elegant, don't stamp.
Go up a cog and increase the pressure slightly, making sure you remain smooth and symetrical.
Watch your knee alignment against the top tube. No kicking (outward) or knocking (inward) allowed.
When you are comfortable stop pedalling with the loose cleat foot down.
Carefully reach down and release you foot from the shoe without moving it from your comfy position.
Release the shoe very carefully using a large flatblade screwdriver to open the pedal (or whatever).
Tighten the cleat, then jump straight back onto the bike for another 10 mins to see if you're happy.

Repeat as required, then do the other hoof.