You should use SoapBox and get the SoapBox team to look into something like the viddler style tagging and comments system.  That way you wouldn't need to split the video's up, just tag the time points and have it as a long video, unless the issue is upload time and such.  Also even better than that when people are watching the video they can comment at the time point so that there is a context to the comment Smiley 

(OK so I'm a Viddler.com fan!)