I went to test my room that I was making, and most of the walls and stuff where not there and where black and when I walked to them I fell down. In the Creation Kit they are there. When it crashed I re opened the Creation Kit and only some objects were there, my exterior (Walls and flooring) Were gone. Only the tables and potions, etc. Were there. How can I stop this from happening?

EDIT: Also whenever I re open the mod I cannot oversave it. It says its in use.

Guessing you're trying to change the mod while the game is running for that last part?

As for the rest, whenever you change something, do a save. Save early, save often...and make sure your loaded mod is set as the active file in the loading dialog. Remember, there's no "Save as..." function, you have to manually set which file you're saving to.