Ok so I was practicing for 1 month to learn how to make mods. I learned much and now I started to make my city. I wanted to work on it for few monts, but I got 1 problem.

Lets say I put 5 houses. I save my mod with name Town.esp. Then I close construction set and tommorow I open up CS again and I load oblivion.esm and Town.esp. After loading I start to add more houses and now it has 8 houses. Now if i want to save this as Town.esp it asks me if i want to overwrite the file, and i want to save the changes but it wont let me cus Town.esp is already in use. So i save it as Town2.esp and I will merge it with gecko. But then other time I remove 2 of houses and edit landscape a bit. Now if i save it as Town3.esp and I want to merge them all , I will have conflict with Town.esp and Town2.esp cus those houses will overlap.

Can someone help me how can i save my progress in making mods?

The CS can load multiple plugin files at the same time (although that's not recommended), so it needs to know which plugin file you want to save to, and it needs to know this before you load the data. That means you have to click the Set As Active File button in the plugin selection screen before clicking OK and loading the data. This allows you to save over the previous plugin.

Ok ty , I think that solves it ^^