Personally, as I have a small collection of parts, they are organised by colour; as I know (roughly or exactly, depending on part) how many of each part I have in each colour, I know where any part is likely to be. It also doesn't take too long to find a part in a small box of only one colour. Any parts I come across during a build I think would be useful are kept aside in small piles, and either used or returned afterwards.
However, this only works because I have a small collection; if you have more bricks, sorting them by type, usefulness or how frequently you use them may be a better solution.
In terms of where to start, I would start with the section I have already thought about how to build, or a section that's relatively simple; that will give you a sense of how large you want to go, and ultimately where to head next. As the cockpit of this model is likely to be more prominent, I would perhaps start there.
But what do I know? I've never built one of these before! My line is smaller, more common vehicles. An entirely different approach may suit you and your build!