Thanks Fred for your clarification and everyone else for the responses. Your answers have been very helpful but to keep the discussion going and to stop the topic straying too far into areas I am not very familiar with (I again apologise for my shortcomings) I would like to reiterate my original question:
How does natural selection favour a mutation that, while advantageous, is not likely to increase the carriers chance of survival or reproduction.
For evolution to work, every transitional step between, say, the light-sensitive skin-patch and the human or cephalopod eye has to be not only advantageous but advantageous *enough* to increase the individuals chance of reproduction. I sometimes have trouble seeing how that could happen, but I suppose it's like Gzus said and every time an adaptation evolves the situation is unique, so there is no single answer.
As for the Dawkins quote, I didn't read it, it's from a television debate, and I agree that you don't need a great understanding of genetics to understand evolution. Darwin is proof of that. Besides that, I admire scientists that are comprehensible and interesting to the layman and I think Dawkins fits this category.