If you are going to use SimpleInvoices in a purely MySQL environment that is fully trusted like in a localhost machine, LAN or VPN or are just intending to test the application and learn about it, then you can use the Single Domain Version.
If you are daring enough to taste the cutting edge and contribute to testing the application, and partake of a multiple database capable rich option set, you are welcome to tryout the Multi Domain Version and keep on wiping it out and re-installing it every few days (yes the dev team is quite active) and enjoy the features as they become available.
The Single Domain Version has been in use for over a couple of years and is reasonably stable and maure enough to be used in a production environment with the following caveats: