I'm just starting to look into this, now that i have lots of free time, thought i could give it a go.

So for example if i have two guitar tracks in a single video, i can put both of them in the same screen, but i can't sync them. I did start the other video about 20 seconds later (that's when the other guitar kicks in), but i couldn't make it sound good anymore. Should i just doodle around with the other track as well from the beginning of the song, and just edit the silent phase out?

Any tips, how do you guys do those videos?
This is how I do it;

1. Setup shitty phone camera
2. Setup my guitar, going into my interface, with a virtual rig in my DAW
3. If I want to play on a already made backing track, I put it on a new track in the DAW
4. Hit record on both the phone and the DAW
5. When the recording is finished, edit, mix, master, record more tracks if I want to
6. Render finished track
7. USB my phone into my computer, take the video file
8. Put the finished track and videos of the take in my video editing program
9. Sync them up as close as I can, using string noise or song parts as a reference
10. Edit to taste, mute the camera audio track, or EQ it if you want to leave a bit of string noise
11. Render vid

You have an opening sync tone striped over every track for sync purposes and usually record with the camera mic as well, then you drop the camera sound after you've used it for syncing the video to the "professionally" recorded audio tracks.