QuickTime is just an architecture – you’re right that you ought to use ProRes. The question will be, which ProRes is best is about two things:
The speed of your drives/system and the quality of your source footage.
The ‘cleanest’ ProRes is 4444 – but it requires pretty fast drives- it’s about 330mb/s
If you use ProRes HQ, it’s about 220 (full uncompressed HD is about 880) – and it’s a decent trade off between quality and playability. You won’t be able to see the compression here.
If I was working feature length, I’d capture at ProRes Proxy (35mbs), edit and then do an online at ProRes 4444.
TL;DR – Probably ProRes HQ is good enough without stressing your system.
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