1) Listen to light - Shoot stills
Work with the DOP to see where the light is and the shapes that are made from it. Maplethorpe isn't a great photographer because he shoots weird naked people, he's a great photographer because he works with angular blocks of light. So once your actors are blocked out, shoot digital stills and put them up on the monitor. Look at the geometry of the shot and use it for dramatic effect (or change it with lighting).
2) PA's
Use your production assistants. They're excited, they're happy to be there, and they'll endure a 14 hour day and come back and do it again. So give them something to do and tell them why it matters. Blocking street traffic matters while you're trying to get a noise-free shot. Getting coffee matters because you're cross-eyed before your fourth Americano and you can't read the shot list. Ask them if they've had a break, or had enough to eat. The answer will be "no" but as a director you'll seem less self-involved.
3) Rehearse, but not too much
Let the actors rehearse amongst themselves at the location, getting comfortable, listening to their voice-throw. Stay out of their way. Then do one or possibly two runs through the scene with you. Not too much. Give them notes, but don't let them rehearse the notes to keep it fresh. Some directors like to rehearse a LOT, so it's a matter of taste.
4) Don't sit down
Director-chairs are cliché. Stand up next to the script super but not too close to the DOP. Let them work, but why should you sit down when your crew is on their feet on a concrete floor all day?
5) Locked master
Just in case it's all going to go horribly, horribly wrong, lock down the camera and get a wide master shot of the whole scene first. That way if technical or personal crap rears its ugly head, you can still keep that scene in the movie. Entire films are made with locked-down master shots. Visually boring, but it's an insurance policy.
6) Block actors with the shot list; clockwise over shoulders
Let the actors see the storyboards just before go-time. Double check the shot list and block accordingly. Then, after your master shot take, you can move the camera over a shoulder and get the first "pup". Move the camera again over another shoulder and get the second "pup". If you have more than two actors in a scene, shoot your over-the-shoulders clockwise. But...
7) Don't break the line
If you cross over the invisible meridian line, your footage will have characters flipping back and forth. In the footage, character A should ALWAYS be on the left, and character B should ALWAYS be on the right. Otherwise your audience will recoil in horror without knowing why.
8) Cat in the window
Okay, so far your two actors have done one with-director rehearsal, one master take, and two pups. You need them to go through one more take with a moving camera, shooting close up of hands, or props, or tie-straightening, or some kind of ambient element in the location (a cat in the window). This gives the editor something to cut away to if a fly goes up the starlet's nose.
9) Don't produce while you're directing
More than half of indie director projects mean double-duty for the director, and writer/director/producer combos are becoming the norm rather than the exception. But while you're directing, direct. Use your associate / assistant producer to handle producer shite while you're shooting. You don't want to be mid-notes with the actors when someone from the location wants to talk about parking or to tell you craft services needs a cheque.
10) Establishing shot on the way out
Don't get your establishing shot when you show up – get it on the way out. You'll have a different understanding of the place after you've been there for a few hours and it will inform your shot. Also you need to spend daylight on your actors. A drive-by establishing shot is the easiest (possibly the only easy) shot to get later if you run out of time.
