Best workflow for video editing?

I'm with Szalam on this ... do the whole thing in PrPro, with one possible exception (discussed later). As to the first place to start, there are a number of excellent learning-PrPro tutorials over at lynda.com, a month of subscription to that would get you a LOT more capabilities and fewer headaches. So often, when starting out, one makes choices that lead down wrong pathways ... and then realize at some point the best thing to do is simply junk the entire project you've been working on & starting over from total scratch. Watch the tut's first ... then start building.

It's in reality a lot faster to getting that project done, and done decently.

Next, looking over this ...

My material is from:
GoPro 3+ with gimbal          -> Timelapse videos, Picture timelapses and "Normal" videos

DJI Phantom 3 Pro               -> "Normal" videos

Canon 500D                          -> Picture timelapses (raw)

Every one of those sources produce video media in "long-GOP" ... short version, it's not just compressed frames, they don't even include full frames except for every 9-30 frames, as all the intervening "frame" data is stored as a data-set of pixels that have changed since the last "I" complete frame. This requires a ton of computing from the CPU/RAM/subsystems setup. Bad enough in 1080, if you're using 4k, it can choke a seriously tricked out $5,000 pc.

So the question is ... whether to use the PrPro "Proxy" media using the Cineform preset on ingestion setup, which works pretty simply, or to create a set of transcodes of the video media for editing (and if 4k, maybe still make Cineform proxies on ingestion). One user here often makes exact-named transcodes from original long-GOP codec media, archives the original (which is vastly smaller on disc), uses the transcodes for editing, but after project completion moves all the project files into the archive folder with the original media and dumps the folder with the transcoded media ... he can re-create it at need from the originals.

Either process is a few minutes of learning, then can be done reasonably easy & quickly.

Now ... I do hope you lowered contrast & saturation some ... but didn't flat-line them to lowest setting in-camera. I shoot GH3, and deal with media from other DSLR cams also. One of the first things a lot of people do is try to emulate "log" media in look, set contrast & saturation to the flattest settings of the camera, and then try and bring back color in post.

DSLR 8-bit media is not the same thing as produced by say a 10-bit camera shooting a maker's Log settings. And if you flatlined contrast & saturation, trying to simply increase both in post may induce tons of artifacts. So ... I would suggest as one of your first test runs, taking a bit of a few clips on a sequence, and seeing what happens when you use the Lumetri Basic tab controls to "neutrallize" that back to normal media. If you post a screen-grab showing the image in your Program monitor and the Lumetri scopes ... probably RGB Parade and Vectorscope YUV ... I'd be happy to offer suggestions.

The "one exception" I have to the use of PrPro ... do you mean your time-lapse images are actually in Canon's RAW format, CR2 or whatever your camera produces? If so, you will need to create jpegs or png from Lightroom or Photoshop first, and import those. Make an export preset that is probably twice the frame-size of your video sequence. Use "Set to Frame size" rather than "scale to frame size" as it will keep all the resolution of the image and you can use Motion/scale-position to "zoom" in and around your stills at your whim.

Neil