I ran a web design agency for 6 years, despite of studying PMBOK for advanced project management (for Engineering projects). I used "Web Redesign, Strategies for Success by Kelly Goto" Courser Link: http://www.lynda.com/Web-Design-tutorials/webredesignstrategiesforsuccess/316-6.html as a basis for building our project management model.
1) Breakdown the project into milestones for your team and for your client example (Finish Wireframes, Confirm on Design Palette and colors, Confirm on Content, Functionality Testing)
2) Include all expected tasks/hours from the beginning, should be increasing with your experience, especially you are focusing on specific platforms, let customer see the different dates in which they are required to provide feedback, even schedule calls with clients on these days
2) Use a robust Project Management tool like BaseCamp, where you can give client direct access to the platform preferably with a Skype/Telephony functionality to schedule calls.
If you need any more help designing and deploying your PM system, I would be glad to help.
