If you're a new beader and have problems with colors I hope this will help you in some little way, if only to let you know you're not alone.
When I start a beaded project, I usually look through my stash of beads, lay out several colors, cull through them and start beading using 3 or 4 colors. As I'm a self taught beader with a tiny little background in art (oil paints and charcoal sketch) I really don't have the whole color theory under my belt or firmly planted in my brain.
The problem that I've run into is that even though the colors may go together when I have them in their tubes laying on my beading mat, when I start working with the individual beads I find that some colors just blend in together and there's little or no distinction between shades and sometimes totally different colors won't show up and "shine" like I had intended them to.
I've found that it helps, especially if you're working in peyote or brick, to make a color swatch with the colors to see how they are going to "play" together. It takes time to make these swatches, but can save you the aggravation of having to take out several rows of your project when you find that the colors just don't work together.
To get me started and remind me how colors can work together I have a color wheel that came in one of my bead catalogs, or I go to Color Theory Basics and study it there. If I print it out, my printer doesn't translate the colors properly, so I have better results looking at it on the computer.
Once I get the colors I want to use in my mind, I have to start looking at finishes. Opaque, matte, silverlined, transparent. Sometimes I think the silverlined will stand out among the others, but in some instances, they tend to absorb the colors around them as the transparent ones do.
I know there is a "science" to color theory and maybe someday I'll be able to use that science to it's fullest, but for right now I just have to start with the basics and go by trial and error.