Don't use Manipulate for this. Instead use a list of images as shown in the documentation for the QuickTime format
http://reference.wolfram.com/mathematica/ref/format/QuickTime.html. This is how you can have finer control over the output.
To make your movie last a certain length of time, you ensure that it has enough frames for the given framerate. Framerate is given in frames persecond. So if I wanted 3 seconds of video, I need 45 frames.
As an example.
frame[m_] := Plot[Sin[m x], {x, 0, 10}]
myFrames = Table[frame[m], {m, 1, 45, 1}]
Export["test.mov", myFrames, "FrameRate" -> 15]
