So, I Premiere Pro. When I start recording my rhythm on the loop pedal, I strike my muted strings 4 times. I use that loop as my foundation for each layer. I'm basically playing each instrument live with my pre-recorded self.
I load up each of the best takes video / audio into Premiere Pro. After I get them on a timeline, I select everything and right click. There's a synchronize option. Click synchronize by audio track 1 or mixdown. The program does the rest.
It's usually pretty good about it, but if it isn't, I use the 4 clicks at the top of the video to get them all perfectly sync'ed up. It's the same reason shows use a slate / clapper at the beginning of scenes. If the program doesn't do a good job, I use the audio waveforms to get them just right.
It's very simple if you have the right tools. (I used to produce and edit commercials, but anyone can do it manually)
Here's a YT tutorial...It's easier to show than to explain: