help for the clueless?

This probably is a totally embarrassing n00b question, but is there some sort of trick or method to avoid your palette becoming a total mess when you color something or paint? Something that people who are not self-taught via trial and error are shown when they learn?

I struggled with this once again recently when I finished my yuletart assignment (btw Yuletart has started posting this weekend so remember to check it to not miss the cool art that is being posted). I can't seem to handle color mixing in an efficient way.

My method when mixing acrylics to color my lineart looks something like this: I usually use two palettes, one for thicker colors (which is not so much a real palette as a largish cookie tin lid onto which I put a layer of very wet paper towel covered by a piece of sandwich paper so that the paint remains wet) and a palette with several depressions for mixing in a more watery way. I also have two containers with water, one that remains clear for making the paint thinner for glazes without dipping the brush in (usually I use eyedroppers for that) and one to use with the brushes.

I put small dollops of the colors I plan to use for mixing on the first palette and start to mix colors and put them on paper. Because for the most part I use acrylic paint in thinner layers I tend to either mix on the first palette until I get the shade I want, put a bit on the second palette, and add clean water until it has the translucency I need, or I add layers of more basic colors over each other on the paper. Sometimes for gradients I also start with less water and then do a wash on the paper. But inevitably after a relatively short while this arrangement becomes a mess, i.e. I run out of spaces to mix or to dilute the paint or both. Am I missing some technique that will make this whole thing more go more smoothly and efficiently?