Generally, we recommend creating a separate Moho file for each shot/scene, and then combining them in a video editing program later. There are a few benefits to doing this:
1. If you make a change to one scene, you don't need to re-render the entire movie, just that one scene.
2. If you want to add, remove, or change the length of a scene, it would be very difficult to deal with the timing issues in your method. If each scene is a separate Moho file, it's really not an issue at all.
3. If you have more than one animator working on the project, they can each work on a different scene if they are in separate files. If it's all one big file, then only one person can work on it at a time.