This is a very broad subject but I'll try to give you some kind of helpful answer.
First off, I'd go with designing the layout of the project (I'm guessing it will be some on screen app, either web or native.) Regardless of color, this is the most important thing. A well thought out layout with easily interpreted elements is absolutely key in this type of thing. The colors could be fantastic but if it has an awful layout all that work will be in vain.
Anyway, find out what kind of services or information your users will be after in this project and make it as easy to find as possible. Generally you want to keep the amount of clicks down to at most 1-2 between each part of the site. Keep things relevant to each other in the same place, and highlight things that are important.
Things like login forms and search boxes should be immediately visible on first look at the site. So should any immediate information.
Next try to think of a general color palette for the project. Something that ties in with what the project is about, for example if it's a "Go Green" or "Environmental awareness" type of thing, pick colors that you'd find outside. Earthy browns, greens, sky blue etc. If it's some kind of corporate initiative then greys, blues and tones of three or four colors would do.
With this palette you need to decide which colors will be used for which kinds of elements. I strongly suggest playing around with services like Adobe Kuler and other palette services to get a good feeling of which colors work together and how a certain color scheme can appeal to a certain service.
When you've decided on element colors, don't be afraid to tweak and change them if they're not working. Don't be afraid to tweak anything at all and especially don't be afraid to tell your client (your boss I assume) that you think and idea they may have is bad. If they want the login box at the bottom of a 1km long page hidden under a smily face that you have to click 4 times, tell them it's a bad idea and why.
After colors and layout comes font. You need a proper font hierarchy, one for headings (two variations, main headings and subheadings) one for menus and one for normal text. Make sure they're readable at their respective sizes and resize well if the user needs to zoom in.
I hope some of this helps, I will of course elaborate on things if you need :)