
There have been quite a few changes from T2 to T3 with the capitals. Here you can find a comprehensive explanation of the T3 capitals.
Your first village is your capital by default regardlessly whether you build a residence or palace in it. Only after naming another village your capital it will lose this status. This can be done by building a palace in the village you want to name your new capital and by clicking the link "Make this village your capital". To be able to do so you need a palace level 1 and have to enter your password to confirm this change. The palace can only be built in one village per account a time, same as in T2.

If you change your capital, the prior capital village will loose all resource field upgrades above level 10. Additionally the stonemason will be destroyed, furthermore the great barracks and great stable will be lost if they existed in the new capital village. Beware: There is no way to undo the capital changing!
A (Capital)-tag marks the player's capital in the village overview resp. the player overview.