Well, the parentheses don't necessarily have to be perfect on the paper :) I can fix them once it's on a computer.

That said, some manual tricks that could help: my former colleague had a simple trick of counting up with his fingers for open-parens, and then back down for close-parens.

I could also imagine using more line breaks and indentation to help keep the parens straight. It might be ugly, but on paper that formatting is only to support my thinking, it does not also need to cater to the committed source code.