Scenariomaking in a nutshell:
First of all, find a topic. Go to the library, rent some book and read up on your subject. Internet also is a great source.
Then...:
1. Start new game on pre-selected map. Chose "King" difficulty, how many civs you want, villages only, don't restart eliminated players.
2. Open cheat menu. Edit kings, treaties, attitudes, civ names etc. Save game. Edit the rules you want to apply for your scen (forbid government switching etc.).
3. Place cities, modify city sizes, cheat irrigation, mines, farmland, roads, RRs etc.
4. Chose what improvements, wonders and units to include.
5. Create a tech tree
6. Connect improvements, units with the new tech tree.
7. Modify unit stats.
8. Cheat improvements, wonders and units ingame...
9. Create Events.
10. Create a readme, edit the other text file (pedia, game etc).
11. Modify the rest of the rules (cosmic rules, terrain rules, governments etc.)
12. Save the game as a scenario in the cheat menu.
Do all of this in the first turn. Do not hit enter. Remember to save and backup as you go.
That's mostly the creation of the scenario (in a nutshell). Then you have to create/find graphics, playtesting and balancing. If you intend to make a good scenario, it can take you hundreds of hours.
There are dozens of great and detailed guides in the 'cradle of civilization' section.
Hope this answers your question.