First of all, I would suggest you to think about what you really want, use the "improve question" widget and add more information. "What" and "How" has to be done depends a lot on your needs and can be very, very different. I'll give you some points to be clarified.
If you want to do that, then I would say it has almost nothing to do with the installator.
One possibility is to create a service in background checking all the time for new updates, but I don't think it is a good idea (I personally don't like software doing that). I think that should be placed at the InitInstance of the program, so it checks for an available update, when starting up.
Once you know if there is a new update or not, you start the routine to download the new version. Once downloaded, the running instance of the software should close. If you want it automated, then you should keep track of where the file was downloaded.
Now starts the tricky part, difficulty is directly proportional to you wishes and how the software is installed.
If all the software-files are in the same folder (for tiny and middle software is the best option) and you don't want a customized install, that's the easiest way. Run the updater, check for previous versions, delete the old one, install the new one.
If the software has some files in the system folder of the operating system or if you want to keep track of installed components and then give the possibility of customized upgrade... that's going to be hard.
Addition after comment 1
Please read carefully. I have told you the steps. You want to popup a window whenever a new update is available, so:
1) create a service that will be executed at autostart and remain in background, checking (let's say) 2 times a day, if there is new update.
2) If new update available, generate pop-up to download
3) When downloading, keep track of the path where the file is being saved
4) once downloaded, check if the programm is running and shut it down if yes
5) (optional) Uninstall your previous version (watch out with common files to other softwares)
6) install your new version (overwriting your previous if you didn't make Step 5)
Addition after comment 2
Create Windows Service