I explored this effect over a year ago for a short film. The overlap of people's heads on top of other people in the row behind them is
extremely tedious to matte out. Imagine tracing the outline of a person for, say, one second, or 24 frames. Now imagine doing that for an entire theater of people.
However...
Shooting the sections in order of
perspective from the camera makes this effect possible. Make sure the only overlap between people is being done live, and by shooting dead on you can successfully trace out the columns or diagonals along the sides of the seats with little to no overlap. Not sure if you follow that...Basically trace straight lines with the camera lens as the origin, and each shot should fill the seats along each line. This way you aren't forced to composite one person over another, only seats, which don't move as much

Similarly, if you are looking for a shot of the audience from the side in the aisle, then use rows. Shooting a tighter shot from the front or back, use columns.
Also it is imperative that you lock down shutter, gain, aperture, focus and white balance. When matting out, remember to feather the matte edge.
Good night and good luck.