Cam,
Are you normally getting a lot of air bubbles when you do your castings? I have done several castings using both flat molds and the ice cube trays. In the past, I've never used pressure or a vacuum, and for the colored, solid castings I've never had a problem with air bubbles. I don't use a lot of catalyst, so the bubbles have time to escape the mixture. When I stir the coloring agents into the resin, I try not to introduce too many bubbles, and when I pour, I try to pour the resin along the side of the container this way I don't introduce more bubbles (kind of like pouring beer or soda, though the bubbles form for different reasons).
The only time I've had problems with bubbles is where I'm actually trying to cast something into the resin, especially something that has texture like snake skin. There, if I recall correctly, the air bubbles tended to get trapped close to the surface of the medium I'm casting, rather than being free-standing in the resin itself. That's been my motivation to try the pressure pots and/or vacuum.
To address your other original question, when you mix the colors depends on the effect you want. If you want something like Ed Davidson's blanks, then you want to mix them while both materials are relatively liquid. If you want something that is more crisply deliniated, then you want to wait 'till the first color has at least gelled, if not solidified, before you add the next color.
Here are two of my homebrew blanks that show the difference in the effects:
http://www.penturners.org/forum/topic.asp?ARCHIVE=true&TOPIC_ID=8925&SearchTerms=polaris
http://www.penturners.org/forum/topic.asp?TOPIC_ID=8371&SearchTerms=resin,polaris