Humtake -
FLC is a standard animation format, HOWEVER, Civ3 uses a non-standard variation. There's alot more info in the FLICster thread (and the readme file) over in the utils forum.
Basically, you have 2 options - You can use FLICster to convert an existing Civ3UnitFlc into a set of 8 standard FLCs (one for each direction, SW,S,SE,E, etc) using FLICster. Then you use a tool like Animation Shop (from Jasc) to edit the FLC. There are some caveats to this approach, documented on the FLCster thread. DarkSheer, who has created numerous great units, prefers this approach because of some of the Animation Shop features, like Frame duplication, transition frames, Easy frame insertion,etc. Once done, you re-merge the standard FLCs into a Civ3UnitFlc using FLICster. you'll still edit the individual frames using a tool like PaintShopPro (also from jasc, integrates with AS).
The other option is to skip the animation tool and edit the frames directly, using the PCX Export option of FLICster. This will create a pcx with 8 rows of animations frames (called a storyboard), or 8 PCX's, each containg one row of frames (called filmstrips) or one PCX per file (called Cels). The variety is to try to make it easy to use with various tools. FLICster lets you view the animation directly from the PCX(s) as you edit, and re-merge them into a FLC when done. This is the approach I prefer, because I don't like Animation Shop. Eventually, I hope to add more features to FLICster to match the useful features of Animation Shop, thus turning DarkSheer from the dark side

. Plus, using PCX files (especially the storyboard format) eliminates other issues having to do with how Civ3 interprets palettes (more detail in the other forum).
Good luck!