To me, a "shooting script" is just a production script--you put the scene numbers in with Final Draft/Movie Magic and that exists to make your/your line producer/any department heads' lives easier.

I tend to do any note-taking and shot-writing away from the printed script. I'll usually have the script printed out and put it in a three-ring binder. Reading through it, I make all my shot notes and story notes and character revelations for page 7--for example--on the back of page 6. Which is lying flat directly to the left of it. So when I'm reading through the binder, I've got the clean script on my right as usual, and the scribbles and notes for every beat sitting there on the left.

It comes down to personal preference, but I would second what Scott said about the financing bit. If this is something you're sending out for fundraising, keep the script as "spec" as possible. Nothing worse than getting an investor who loves the project but feels intimidated by all these shot descriptions and SMASH CUT's and decides it makes him insecure enough to take his money away. I'd lose sleep over that one.

Thank you both! I have been writing as if it were a spec script. That helps me see if the story is working or not. I asked my question because I was finding translating my set of scripts (for a web series) into a production schedule challenging and was wondering if there were things you could do in the writing phase that would alleviate this difficulty (as simple as something in the slug lines). But no, that's just always a challenge. :)

And Nate, re: the binder, I totally do that too! Though I mark up the script page too... I'll try your specific approach now.

People making shooting their own scripts might want to give Celtx screenwriting software a whirl. It's free open source and it has a lot of production coordination tools built into it.