1- scout your locations and take pictures. Since you shoot with your DSLR, you can immediately get a sense of what is possible with your lens. How wide can you shoot, how close can you shoot?
Where are the windows, doors, where does the sun move, etc.
Make a simple map of the location.
2- make a storyboard with the floorplan in mind.
Keep the drawings simple but clear, so you can show what you mean.
Improvising can be fun and tempting, but it can be smart or unwise. Sometimes improvising just takes a lot of your time and in the end you find out you forgot things, because you ignored your own planning.
You can now note camerapositions at the shots in your storyboard. These position can be drawn on the floormap. This way you can also plan the best order of shots and camerapositions, so you don't use too much time moving around.
You can't read any Dutch, I guess, but you can still look at the video and pictures on my blog about how I created a animation from a storyboard. I know the storyboard is rather crappy: I didn't have to make a cleaned up, better version, because I was the only crew reading the storyboard
http://brokxmedia.wordpress.com/2010/07/01/anatomie-van-een-zomergroet-storyboards-deel-1/
3- 'only the lens is reality'. Anything the camera doesn't see, isn't happening. From one side things may look great, stupid or genius, but if it's not in the frame, it doesn't really matter. Get a cheap portable DVD player with screen with composite inputconnectors. It may not be the ultimate way to judge color, sharpness or brightness, but you can see what is happening.
Your miscommunication could happen because you threw away the visual aid you had (storyboard) and didn't look how she interpreted your instructions. You are both not very experienced, so it's very hard to talk about visuals and understand each other.
Going over the storyboard with the DP before the shoot is a good idea as well. You can ask for suggestions and you can see whether there are shots that don't seem te work.
BTW, I think she made a good decision on the choke shot: not only is overshoulder a common way to shoot things: it gives more depth to the image and probably adds to the action and anxiety of the 'chokee'.
(Let's hope it fits in your edit.)
Another example from my blog is about the illusion you can create with a camera. (It's about a bed, while it's not a bed. But you can also see the external monitor we used: a Philips portable DVD-player.)
http://brokxmedia.wordpress.com/201...-de-schermen-bij-de-opnames-van-de-paasgroet/
(4-) rotoscoping the lights out of one take and putting it into the other take is a bad idea. It will take you too much time, a dozen new indietalk-threads, a lot of frustration and poor results, because you'll find that both camera-angle and movement won't match.
Edit the darker stuff and edit the reshot stuff and look which version works best.
Good luck!