Prearing the guitar is one of the most important steps so its really needs to be done correctly. If you dont make sure your happy with the prepared guitar then you will only regret it if you then swirl it and decide to keep it.
And remember, before you dip your guitar practice, practice, practice!!!!
As this site is aimed at the swirling process Im not going to go into the full preperation steps but one of the best guides out there (the one I used) can be found at the following link.
If your swirling a guitar from scratch (bare wood) the check out this tutorial on preperation. Its very good with lots of excellant tips.
Once you have prepared the guitar body there are a few other steps you need to take before taking the plunge (sorry had to get that one in there).
Spraying the guitar with an undercoat color will change the way the swirled colors will appear on the guitar. The paint that gets transfered onto the guitar is very thin and is fairly transparant so its advisable to test out differant combinations so you can see what the final effect will be.
In the past I have found that if you decide on the swirled colours then undercoating with a lighter version of the lightest color is generally best. As you can see in my GMC swirl I have undercoated the guitar in a light green, this helps to bring out the green color and hides any areas which either did not get covered with any paint; or areas where the paint was very thin.
The folllowing site will help you understand how colors might affect the final colors.
Once you have the guitar the color you want to dip with you need to make sure that the water has as little opportunity to get into the wood as possible. The body should only be under the water for a few seconds but why risk problems later on.
You can put anything in the holes as long as it fills them and is waterproof, a few suggestions however would be:
If you cannot find anything then you can always just half screw in the actual screws which go into the holes to plug them up. I tend to not mask off the full cavities though as they will show when the pickups etc are in there.
Finally you will need to make a temporary neck to hold onto when dipping, anything will do but its easiest to use a bit of wood and just screw it in place through the neck screw holes. Make sure the temp neck it attatched firmly though as it will have pressure on it when its under water (as the body will be pushing up trying to float to the top).