thing is if you focus on something up at f1.4 the depth of field is going to be so thin that everything not in the exact same plane as your focus point will be, well, out of focus. You can do lovely arty bokeh shots like this. Like focusing only on one detail such as a logo etc. while everything else blurs away.....
At f16 you will have the depth of field to get a lot more in focus but stopped down so far you will need a much longer exposure and hence the tripod. Aperture priority will set your shutter speed for you if you select the fstop.
don't get me wrong the 50 will provide perfectly great results and the resolution of the 5DmkIII means that you can crop stuff at will and maintain a good size for publishing to the web.....
Shooting into a case is quite difficult actually....I have tried it....I resorted to having the camera on the tripod and just to one side a diffuse shaded table lamp for light so the shadows are almost cast from the same place as the lens is pointing and so don't show up. (i.e. lens and light source almost at same point.... and you know what, I'm damned if I can find the pics....annoying....but they were quite good honest!
I kept ISO at native (which for the D700 is 200) to keep noise down and just shot long exposures via remote to eliminate shake......you have your iPad for that....