1. Open the CK
2. Click File Menu and do DATA - Check skyrim.esm and update.esm
3. Click File Menu and SAVE
4. (The file you saved just became the "Active File")
5. Now make any changes - to anything - and they will be saved in that file.
(When starting Skyrim game, click Data Files on the loader to check that your mod-file is loading)
Note: SHUT SKYRIM GAME BEFORE DOING ANY MORE EDITING (some people will give you a workaround for that ... but I think it's better to have it shut, just in case)
Next time you open the CK and you want to continue your work:
1. Open the CK
2. Click File Menu and do DATA - Check skyrim.esm and update.esm
3.
ALSO select your mod-file in the list and click the MAKE ACTIVE FILE Button
4. Now make any changes - to anything - and they will be saved in that file (and all your older changes will still be there)