How to use EEPROM to save my settings value while the program is running.

I'm not getting the idea how to make my Arduino wait.

Why should it wait? You posted on the forum. Are you sitting in front of your computer waiting for a response? Or are you able to do other things, like breathing, sleeping, and/or eating, while periodically checking for a reply? When you DO get a reply, can you remember what the question was?

Well, write your program the same way.