I've been watching lonlonjp's videos on youtube for a while now (surely, at least some people around here must be familiar with him)

And after trying to play some relatively easy tabs (like Red Wings, for example) I noticed something he can do and I'm clearly missing...

On quite a few of his songs, it appears as if he's keeping a rhythm with his thumb and a separate rhythm with the rest of his fingers. Sometimes the beat coincide, sometimes they don't.

The question is... how the hell do you do this? obviously the answer includes "A metric shitload of practice", but how do you even begin practicing towards that?

This one is probably one of the most notorious: http://www.youtube.com/watch?v=61a-UNZwpNk&feature=relmfu

But there's also http://www.youtube.com/watch?v=o1sYOi8Bfl8 and this one: http://www.youtube.com/watch?v=p1tS7KNJHvc
I would suggest really working out solid rhythm with your thumb first. Then incorporate simple fingering. Start s-l-o-w haha. Good luck!
I honestly doesn't see anything hard or special at the video you gave. he's just playing a constant open bass strings and sometimes he frets them.
though the video fingerboy gave is totally something different. though it seems he uses a technique somewhat similiar to sungha jung version of "wake me up when september end". that might be a good start
He's playing the bass strings constantly, usually on different beats than the ones on which he frets other strings, which most of the times but not always, fall on the same beat as the bass.

Granted, I'm pretty bad at rhythm atm, but even slowly I couldn't really get it to sound like that.