If you want to use the film viewer shots, then save them as uncompressed AVI's, and then use a video editor, such as Sony Vegas, to put the pieces together.
There are pros and cons to every approach. The film viewer allows you custom camera positions and paths in the output, but it does not record audio to the output. The film viewer will also create perfectly fluid videos, regardless of the graphic stutters you might have in the original recording.
External recorders do record the video. As they grab the rendered frame, they also benefit from any anti-alias setting. The film viewer does not. However, you can work around this. By creating all the video in 1920x1080 (or higher), then sampling down to 1280x720p in the output, it will soften the edges.
All the videos we have on our Youtube channel were done with a combination of Sony Vegas Pro, Aces High Film Viewer, Fraps, Adobe After Effects, Adobe Audition, and some other programs.
There is no single "best" method for video work. It really starts with what you want to accomplish. The tools will usually reveal themselves when you decide on that.