You have several very effective weapons with which to combat the increasing complexity of your design. The first and most effective weapon in your arsenal is documentation. Write it down. That's all it takes. It doesn't have to be fancy or even very detailed, but it does need to be accurate and as complete as you can make it.
Pretend that you're actually still going to be interested in this project in three months and may want to go back and understand “Just what was I thinking?” at some crucial point in the design process. You'll most certainly need more than some arcane program sketches and tangles of wire to figure this out.
Better yet, pretend that someone else will take an interest in your design. For all you know, they may ...