By default, AceText automatically saves your AceText collections. It saves them not only when you close AceText, but every five minutes. This way, you never lose any data, and you never have to worry about clicking the Save button every so often.
When you click the Save Collection button on the main toolbar, press Ctrl+S on the keyboard, or select Collection|Save Collection in the menu, AceText will ask you for a new file name for the collection. You can either choose the same name, overwriting the existing collection, or a new name. If you pick a new name, the automatic save will work with the new file from then on. The original file is no longer used by AceText, until you decide to open the original again.
Basically, the "Save AceText Collection" button works like the "File, Save As" menu item in many applications that do not automatically save your data.
If you do not like the automatic save, you can turn it off in the Files Preferences.