First thing you should know - all updates are free during 6 months after your purchase, you may update as many times as you want within this period of time.
If you like you can prolong update period by purchasing Update Service for 6, 12 or 24 months - see product order page.
The best way to update is to use this notification:

Click on it to download newer version.
Store Manager check for newer version every time it is started.
To turn on/off this check change this option:

Also you can find download links of recent versions at: http://license.magneticone.com
Click here to find more on "How to get recent updates of Store Manager".
You may install new version over your existing one, all connection settings and other information will not be changed. If you uninstall your current version and then install newer you may need to register again.