Overnight stop selection
To set a place as an overnight stop you should make sure it is one of your intermediate places when planning the route. Then open the drop-down menu for that place (the little icon to the left of the input box) and select "stop here". To turn stopping off, open the menu again - it will have changed to "Clear stop".
Then "Calculate Route". That's all you have to do.
As yet there is no way to choose which night you want to stop (it will be the closest night to when you would have passed through the place if it hadn't been set as a stopping place), to select anything other than a single night's stop (neither 3 days nor a few hours) nor to avoid strange effects on day length (so, for example, if you have 7 hour days, and force an overnight stop at somewhere you would have got to after three hours travelling on the second day of your trip, you will end up with a 10 hour first day). All of these are likely to be worked on in the near future.