I'm writing a story, and I'm finding myself getting lost so easily. I was considering moving it to a different tool, like twine, just because of the graphical map of all sections, but I'd prefer to keep using the squiffy's syntax, because I find it to be much more simple and doesn't break my creative flow when writing.

So, I got curious about how you deal with it when your interactive fiction gets too big in squiffy.

I do a few things, but one thing that comes to mind is creating a large amount of spaces between major sections. Then, when I run through the code, whenever I see a large space, I know I'm entering another major section.

DM Bluevoss. He's the master of looooong and excellent Squiffy games.

Or just look at the source code of one of his games. Google mrangels "desquiff" tool for that.