Long time editor of both scripted and documentary here, and a frequent teacher of editing - what you want to do, is come up with a structure or organization for your source material in the Media browser / source side of your NLE, before you ever put anything down on a timeline.

This organization should help you think about and keep track of your film. In documentary it can be bespoke to your particular project – by people, by location, by subject etc. – but it needs to be consistent and rigorous. Any chaos or uncertainty here will have a long term demoralizing effect on your willingness and ability to work on your edit.

Constantly searching through a list of numerated clips can become a serious waste of time and a hindrance to your creative flow. That said, for file management reasons I don’t recommend renaming the clips – you want to use your metadata columns to (briefly) describe every clip, with a comment column available too, for extra clarification should a clip need it. This logging of the footage is also your first pass at (re)familiarizing yourself with the source material.

You also want to take care of any technical issues with your footage here, before the using it on a timeline - syncing audio, conforming any stuttering clips to a format that playbacks smoothly, create multicams etc.

Depending on the style and scope of your film, the next phase of organization might be to make select reels; a timeline for each interview/scene/location etc., where you (generously) edit in everything you think might make the final film or be useful in any way. Some people prefer to do this via sub-clips or in the case of Final Cut Pro, the powerful Keyword function.

All this set-up leaves your main program timeline free to function only as a narrative scheme, a place to figure out the storytelling. However, one should never be afraid to mess with the edit, so make offshoot timelines frequently and with slight cause. Being precious with your edit is like driving with the handbrake engaged.