I've been using a video camera to do timelapses, but was planning on using my DSLR this coming season. I've been doing most of my shots at 16x, which is just over a half second per frame at the framerate I'm shooting at. This works well for structure. For a long lived, and slow moving tornado, 4x or about a frame every eighth second works well. Obviously you'll probably want to leave most of your tornado footage at normal speed, but if you've got 20 minutes of tripoded stovepipe from afar, that's going to be tough to sit and watch even if you love tornado video. The DSLR probably can't keep up with a framerate that fast though, or at least not for very long. I'd suggest varying the shooting speed depending on the situation, with a fast moving gust front and structure that's overhead at 0.5 - 1 seconds per frame (or as fast your DSLR can shoot continuously), other structure shots at 1 - 2 seconds per frame, and distant structure, slow moving clouds, and night timelapse at 2 - 5 seconds per frame. Those longer gaps will let you run longer exposures for low light timelapse shots too.
I was planning on shooting in manual too. I haven't done any experimenting yet, but I imagine there is going to be some flickering or at least uneven shifts in brightness if you let the camera pick the exposure length per frame. If you're shooting raw you'll have room to play with tweaking the brightness and doing some smooth transitions in post processing.