If you look http://cs.elderscrolls.com/constwiki/index.php/Category:Settings, you can see a full list of in-game settings. These can be accessed and changed from the Gameplay --> Settings menu in the CS.
To change the names of skills, these are the ones you want to edit:
sSkillNameAcrobatics
sSkillNameAlchemy
sSkillNameAlteration
sSkillNameArmorer
sSkillNameAthletics
sSkillNameBlade
sSkillNameBlock
sSkillNameBlunt
sSkillNameConjuration
sSkillNameDestruction
sSkillNameHandToHand
sSkillNameHeavyArmor
sSkillNameIllusion
sSkillNameLightArmor
sSkillNameMarksman
sSkillNameMercantile
sSkillNameMysticism
sSkillNameRestoration
sSkillNameSecurity
sSkillNameSneak
sSkillNameSpeechcraft
You may want to peek around at various text snippets, such as skill descriptions and the like, and alter those to mirror your changes.
You cannot add or remove the skills themselves, as they are hardcoded.