So I did some research about project management, and found that people have recommended various ways to arrange stuff and I'm trying to establish the best practice for myself for the whole process. Some say to have a separate blend file for each shot, whereas some say to use blender scenes, so that means having multiple scenes in one blend file, but to use dynamic linking and group instances to reduce memory space. I feel they both are kind of extreme. I was thinking to have 1 blend file for each scene. This means that if I have say 4 shots in scene 1, I will have all related assets arranged in one blend file. But, since this is my very first project, I am curious as to how will I merge everything. Say, i setup my cameras, lights, and got shot 1 animation just right. Should I render it in png's right away, before I move to next shot, or should I keep all shots sequentially arranged in my timeline animation in one long track since it's all going to be in one blend file?
This is my personal preference and you will find this with every answer as each person does it differently dependent on computer power and their work method. Please keep this in mind :D
I would go with keeping scenes in separate blend files as it can stop any accidental cross-contamination of scenes. It also leaves layers free to hide items and create layering if need be.
You may find having multiple scenes in one file will slow blender down significantly.
When you render, save it as png frames so you can go back and check it. If something is wrong, you only need to re-render those frames, not the whole scene. It may take a lot more space, but it may save you time. Separate the scenes into different folders so there is no cross-contamination.
Good luck with your project and I hope I helped,