This is the way I've been using Channels DVR so far:
- record programs with the DVR
- use Avidemux to manually remove commercials from recordings without re-encoding
- move the clean recordings to Plex for viewing
My recordings are 90% from TV Everywhere so the video files are H.264 in MPG containers.
Using Avidemux works pretty well, especially without re-encoding the videos. No need to re-encode since the recordings are originally already compressed in H.264 at the source.
There are times though when it is a bit annoying because you can briefly hear half a second of the end of the commercial break at the very beginning of a new segment of the program when I cut the videos. It seems to happen mostly with recordings from the Hallmark channel. It's just the sound, not the video. I'm a perfectionist so I wish it was cleaner.
I'm not sure whether it's an issue/bug with Avidemux or not.
So I've been looking for alternatives for removing commercials. I found LosslessCut but it turns out that it doesn't support the TVE format natively and that slows down previews. It's so bad that for me it's unusable.
That brings me to VideoReDo that I've seen mentioned around here. I haven't tried it yet, I've only watched videos on YouTube so far. If this tool is better than Avidemux for removing commercials without re-encoding, I don't mind spending the money for it if it makes my life easier.
It's not very clear to me whether VideoReDo can cut videos without re-encoding. In the last video that I watched, it seemed to show that it was encoding but in the process I caught messages saying "fast frame copy" so I'm not sure.
Before I spend (waste?) time on it, I figured I would ask Channels users directly how you actually use it. Maybe provide a step-by-step guide, if you don't mind. 
Convince me to use VideReDo. 