hi brooklyn,
clip
is a technical definition of a part of a TVPaint project. Every clip have its own timeline, where you create your drawings/frames. Your project always have one clip, when you start a new project. You can add clips and can change the order of them in the project tab.
scene
is a possibility to sort your clips in the project tab. For example, when you have 6 clips, you can put them together to different scenes to get a structure in your project. Clip 1 and 2 become scene 1, clip 3 become scene 2, clip 4, 5 and 6 become scene 3. You can think it a little bit like the structure of a typical movie: shots, sequence/scenes, act.
If you are using TVP 9.5.x you can read about clips and project tab under the help menue / what is new in 9.5.
It is not possible to use different framerates between clips in one and the same project. I think, it don't makes any sense anyway. For example, when you make an animation for a PAL Video-DVD, your speed (framerate) have to be 25 frames per second. If you want to make your animation faster or slower, you have to change the timing of your animation. Add more drawings or double some frames (working on 2's or 3's or 4's for example), or to get more speed, remove some drawings.
Here is a closer look about animation timing:
http://www.connectedconcepts.net/craft/ ... -part.html