The hardest part of starting any project I’d say would be, well, starting it! You have your ideas of how the end product should look (the “B”) but sometimes, as often is the case with web projects, the “A” can be tricky enough before you can even consider getting well and truly under way.
I often resort to prototyping stuff on paper, purely because technology then cannot get in the way to distract your thought processes. Sketching out how the overall site shall look and then digging deeper into the idea to work out how each piece of the puzzle will work.
I don’t use tools like visio or any of its equivalents as they confuse me straight away and distract from the brainpower needed to do the coding. Pen and paper still wins for me. They are so portable and need no batteries!
Design is a crucial stage in any project and whilst you may be designing something of a technical nature, as I am at the moment, ironically it’s best to avoid using complex methods for system design.