There are entire books devoted to this topic.
1) Familiarize yourself with design patterns
2) Start by sketching your GUI on paper - try and discover any caveats
3) Using your visual GUI sketches, start designing your DB schema - normalize it.
4) Begin coding your HTML templates based on your visual sketches
5) Begin developing the model code
6) Begin tying your interface to your model.
7) When step 6 becomes to complex refactor into proper MVC separations.
Reapt until finished and voila - a complete product