The key thing is to come up with a crisp definition of what you want your final product to do, and for whom.
Also, bear in mind that an encoder is exactly software that analyzes a source and attempts to adapt encoding to get the best results of it. There isn't always stuff you can set manually than the encoder can do itself. It really depends on your sources and your goals.
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Ben Waggoner
Principal Video Specialist, Amazon Prime Video
My Compression Book
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