Alnour,
I'd set up seperate seed files for modeling and drafting. Layering convention, colors, etc can simply be thought of as your company's current 'convention' or how your currently doing things. Now just write that to paper and everybody should be following it. For example, everyone abides by: components being on layers 1-50, construction geom on layers 101-135, each part will start with a datm csys on layer 100, colored white, and all sketches will be attached to this and be on layers 136-180. Things like this...
Your company CAD standards should be followed, and if you don't have any identified than thats the first place I'd start.
SS