this is an interesting idea, why design agencies? What are they like? Is it so I can offer a technical expertise to their design projects?
Do some research in your area to find a fair hourly rate for your work. Bill hourly, never ever agree to a per-project fee, I cannot stress that enough.
Also I would recommend against accepting any offers of full or part-time employment with the agencies. They tend to be sweatshops. Treat them as a supplementary source of income and don't get sucked in too far.