I usually keep things as organized as possible... it makes pre-production a bitch, but production will go by smoother.
Here are some tips to make things better for ya!
I) Devise a shooting script - screw official guidelines of how a shooting script will look... take your script apart, organize by location (or whatever you want)... so if you shoot 3 scenes in a car, 10 in a house, 5 in a garage, 4 in another house shoot it like that... don't try and shoot it in the order you wrote or you'll be back and forth.
II) Make sure if you're shooting at night for exterior shots to get on location 15 minutes (or more depending on equipment and such) to prepare... you don't want the sun rising in the background of your midnight chase scene... or maybe you do?
III) Keep a notepad, scribbler (oh yeah old school), clipboard, etc with you when your writing and write down and extra descriptions you want to remember.
INT. SAM'S KITCHEN - DUSK
SAM stares through the window that overlooks his backyard, he notices what looks to be a person walk just behind his garage. SAM heads for the door to go out and investigate.
So that's your scene... on your notepad you might write down
"Low angle shot of Sam looking out window" ... "EXT shots will be shot indoors through window to simulate POV (point of view) of SAM"... "remember to color correct ext shots to get that dusk feel"... "pick up milk at the store"... etc.
You want to keep your first drafts of your script cleaner so when you begin your later drafts you're not swofting through paragraphs of camera movements and extra notes to try and remember where the hell Sam put that butcher knife in scene 46.
IV) If your not already familiar, get familiar with your editing program... learn what you can do digitally and what you'll need to do physically. Also practice all your special f/x and such... do your homemade squibs work? Does your fake blood show up well on camera? TAKE TEST FOOTAGE! Does that stabbing effect look cheap on camera? Work around it!
V) This is more of a production step, but nonetheless! Prepare for multiple takes... get extra film. You want lots of coverage so when you edit you aren't going to be stuck trying to fit in a goofy take because you only have two to work with.
VI) Make sure you have extra batteries, your cables and cords are labelled, your notes are in order, etc.
VII) Prep your actors, have a read through... Sometimes when your in a pinch to finish a shot you'll start to accept crappy performances to keep the flow going. Try to avoid this by letting your actors know ahead of time what you'll expect in every scene... give them a copy of the script to take home, make notes with, etc. Nothing sucks more than having to take 36 minutes to light a 2 minute scene that you only have 8 minutes to shoot and your actor is stiffer than a 2x4 and can't remember his 1 minute monologue that consists of 3 lines, a yawn and a Smurf reference.
It's a lot of work, but it'll keep things running smooth... also it'll get you and your crew and actors prepped for when you guys are all in Hollywood doing the big movies!
