OK, so if you set it to zero and it'll keep shooting forever and ever; or until the card is full, whichever comes first, where's the problem? Is it that you're trying to capture a specific number of frames to fill a specific timeline in the video? If so, got a watch? I never set a specific number of shots when I do timelapse work. I just let it go and time it with my watch. I know what frame rate I'm going to produce the video at, I know what interval I have between shots. Based on those two things, I know how long I need to shoot in order to get the right number of frames. Easy.
That said, Canon's hardware blows chunks for timelapse work. It truly does. I know you've already bought an intervalometer so may not want to drop more money but the Promote Control
is really the best option for Canon shooters who want to to timelapse and/or HDR timelapse work.