How should I write the guidelines for the design (colors, dimensions .etc) for the front end developer to use?
At the moment I just create an overlay on top of my design and write notes in that overlay.
How do you do it?
What most people do in this situation is to provide the developers with a pattern library / design library /style guide. This is what I provide the developers at my company with.
Its basically a wiki that shows the developer what they need to build out say the navigation for example. It will provide them with all the information they will need to remake your design so that it meets your design requirements. Its up to you how granular you think you need to be to get these guys to successfully understand how to remake your vision correctly.
Here are two examples: http://ux.mailchimp.com/patterns http://www.starbucks.com/static/reference/styleguide/
Good article to read: http://alistapart.com/article/creating-style-guides
If you don't like doing it on a layer (which sounds fine to me), print it out and mark it up by hand.
Somehow you have to indicate an object or call it by name and write a list of characteristics describing it. Whether you do that in the program or on paper is up to you and your developer.