Yes, the procedure Marc described works well with Cheetah, too. But that’s about creating a new animation — I thought the OP was asking about tweaking existing animations.
I’m still pretty much a noob at this stuff myself, and it seems I misspoke before, so I want to try to clear that up.
Cheetah3D does load all takes in an FBX file into separate takes within C3D, and writes them out as separate takes too (which Unity sees as separate animation clips). The problem is other modeling apps — it appears that the vast majority of them don’t support more than one take per file. So either they write out each clip as a separate file (usually with a complete copy of the mesh in each one), or they write all animations out as one giant take, and then carve this up into separate clips within Unity.
When you get a model from the Asset Store, it will often have many choices. As an example, I recently bought the Dragon model from 3dfoin. It comes with iClone, Blender, FBX/MAX, DrEse, OGRE, RC, and a Unity package. Some of these, like the DrEse (whatever that is) folder, contain a bunch of FBX files — one for each animation. Others, like the FBX/MAX folder, contains a single file that contains all the animations in one giant take, plus a text file that tells you which range of frame numbers correspond to which animations (stand is from 0-40, idle is from 42-342, etc.).
The Unity package contains the same single FBX file, plus the textures and materials and such all set up for use in Unity. It also has the animation clips already defined on the model. But these animation clip definitions do not appear to be actually stored in the FBX file itself — they’re part of the Unity import data, and appear to be stored in the .meta file that’s created next to the FBX.
That’s why, when you load this FBX file into Cheetah3D (or any other modeling app), it doesn’t see the clips as different takes — they’re not different takes, and there’s nothing your modeling app can do about it. So you either have to tweak the animations in one giant clip, or load one animation at a time from of those formats where each animation is in its own FBX file. Either one is a reasonable solution, I suppose, though neither is as nice as having all the clips available as separate takes in one file (which you can do if all your rigging and animation are done in Cheetah from the get-go).
Hope this clears things up, and sorry for creating confusion earlier today!