You disconnect all the hoses, and in my case they were out of the car, so I just filled them up with brake parts cleaner, shook things around for a few minutes, drained and repeated until clean. In the case of those thing which don't come out (e.g. evaporator), you fill it with a couple ounces of solvent using a hose/funel, connect a drain hose, and go at it with compressed air. For me, my lungs and a hose provided the source of air. Just be sure you don't breath in through the hose
You don't flush the compressor, just drain it by turning the shaft and tipping it over. If you're planning on doing a thorough job by flushing and installing new Orings, and new accumulator, you can use PAG oil with the r134a. You wait until the last minute and spread 7oz around evenly (2oz in the evap, 1oz in the accumulator, 2-3 in the compressor, 1 in the condenser). Leave the accumulator sealed until the very last. Hook it all up, turn the compressor by hand 10 times or so, and hook up the vaccuum pump and let it suck dry for 45min-1hr. Turn the pump off and wait for another 30min to see that it holds the pressure. You don't want any leaks. Then you can either charge it yourself, or have it done. You can wing it and shoot from the hip with the kits; bleed the hoses, charge into the vaccuum as much as it will take. Then start the car, turn the A/C on Max/Norm with the blower on full and charge with 32oz of r134a. Thats 80% of the original r12 capacity which is what they recommend. You'll need to rev the engine to about 1500 RPM to get all the refrigerant in. Don't put in any more than 32 oz without a set of gages. If the high pressure line is too high, you can overcharge it and have a problem.
If you do it right, you won't have any problems. If you forget a step, then its a risk you take that a leak could form. Leaks let air in and wet air+r134+PAG chews holes in things.
Be sure you use mineral oil or Nylog on the Orings, not the PAG.
The folks over at
http://www.aircondition.com/wwwboard can answer any other questions you have. They're rather busy, but the archives have everything I discussed.