A few things I'd suggest, since no one is really going to see this beyond cast & crew....
1) any time you use a special prop, effect, etc in the script while writing it, CAPITALIZE IT (this used to be something of a standard practice in hollywood, too, though most writers don't bother with that anymore - there are departments to do that). This makes it stand out, which, believe me, is a help when rushing to a new location / setup / whatever and behind schedule (you
will be behind schedule at some point). It really sucks to drive, say, way up into the mountains, start shooting, and realize no one noticed that they were supposed to bring the critical prop. Even better, buy one of those huge sets of multicolored highlighters and highlight everything, color-coded -- one color for wardrobe, one for props, one for vehicles, etc. (In major productions there are semi-standard colors that are used for this, but it's done by a "script breakdown" department, and the writer never really sees it. On an indie shoot, it'll help a lot if you write with this in mind in the beginning, though)
2) Any time you're thinking you might want a new shot within a scene, treat it as a new scene. This will help enormously in figuring how long it will take to shoot. Every new camera / lighting setup is effectively a new scene in terms of how long it takes to prep for.
3) Storyboard shots. Even if its just crude stick figures and arrows on notecards, it helps everyone understand what's going on and what their job is.
4) A note on estimating times to shoot scenes... if this is your first project, take the amount of time you think it will take to shoot a scene, and triple it. Now double that. That's about how long it will take you
5) Also, more along the lines of actual shooting, I have one word:
coverage. Shoot lots. Especially if it's digital, where more minutes of footage cost almost no more than less minutes of footage. Allow at least five or six minutes of shot footage for every minute you use. More is better. Take wide shots, close shots, different angles, even bracket f-stops if you're using a camera that lets you control that. You'll be amazed how much that matters in editing, even if you
think you know exactly how the shot should / will look when done.
Those are the biggest tips I can think of for now.
Oh, and two other points I can think of, totally unrelated to writing:
A) The number one reason films are denied competetive admission to film festivals? Poor sound quality. Even if no one else on your crew knows what they're doing, make sure your sound guy does.
B) Food. Seriously, I'm not kidding. A shoot can be exhausting work, and nothing saps a crew's energy like hunger. Make sure you have a variety of food, decent food, on hand at all times. On an indie shoot, where you're frequently asking the impossible of cast and crew and friends for little or even no pay, food should actually make up a significant percentage of your budget.