The choice of which settings to apply in camera has been the cause of some confusion on set.
1. Remember that the settings of which colorspace to view the footage in are only in-camera "looks". They are NOT applied to the raw footage - the .R3D file. They are encoded in the meta-data so you can retrieve them a variety of ways in post.
2. The in-camera settings DO affect the meters and scopes and Zebras.
Use the colorspace and the meters the way they were intended - as visual guides to approximate post-production output.
REC 709 is a Broadcast television colorspace. Its colors are clamped at 100 IRE. If you know that your primary market will be Broadcast TV - like a television commercial - you should probably set your viewers in REC 709 and leave them there. then when you check your Zebras and other meters, they will be representative of your output.
Redspace is a logarithmic colorspace. This means that it will appear dark untill it is correted. This is not something to be worried about. Anyone who has ever seen 35mm film dailies knows that the saturation and other color space information will be greatly changed in the post process. If you are shooting on a RED and are going to be outputting to film - you will want to leave you meters in this space. Trust the numbers, and you will train your eye.
Mixed Usage - if you are shooting a low or medium budget project that will go direct to DVD without the need for theatrical release - then you will find occasion to jump back and forth. This is because most of the viewers will watch on TV and REC 709 is a pretty good approximation of your DVD space. In reality you have more headroom on the DVD than you do in broadcast - so if you shoot for broadcast - you will be safe for DVD.
Special Shots - There may be those cool shots where you really want to push the exposure latitude - ie. shoot from inside a room and see something outside the window on a sunny day. Under these circumstances - switch to the RAW space. This will give your meters the full lattitude of the Mysterium sensor and you can max it out. Make sure you know what you are doing. Overexposing in the digital world is 1s and 0s. If you go into Superwhite by 1 IRE or 100 IRE you will still NEVER be able to extract ANY color information from those pixels.