I've always been a little confused about which skills are safe to use when programming actions in Lite-C. I know in the manual it says what the ranges of skills are used for (ie: 1-20 in WED properties, 21-40 from deprecated A6 template scripts, etc.). When is it not safe to use a certain skill number?

If you don't plan to use any templates you are free to use all skills you need for whatever reasons or purposes.
I oftentimes do the following: I use the first 10 or first 20 skills to set the properties of entities with level actions in WED, then I keep skill40-skill49 free so I can use them for shaders later on and skill50-skill100 get redefined (such as #define _type skill100). The remaining skills are used (in my case) for temporary calculations and the like.