I don't think that this can be done through Empower alone.
You can setup a pause time, or you can equilibrate at flow 0 for a certain time, but in this setup you have to calculate manually (or through a spreadsheet) the required amount of time.
Another possibility is to use visual basic or another program language that either controls your mouse pointer and buttons, or can push buttons.
If you then use the task scheduler, you can use the program to load your sample set and push run.
Yet another way: use the Empower toolkit in combination with the Windows task Scheduler, but I'm not sure if this is really possible without buying add-ons.
Ace