If I understand your post correctly, you have devices on your internal networks (LAN) that communicate with a database server located elsewhere on the Internet (accessible via your WAN).
If this true, then you need to simply add the IP address of the remote DB server to a Pass List by creating a list on the PASS LIST tab, accepting the default checked options, adding the IP address of the remote DB to the list using the controls at the bottom of the EDIT LIST screen, then save the new list. Now go to the INTERFACE SETTINGS tab in Snort for your WAN (since your are running Snort on that interface) and select the newly created Pass List in the drop-down selector there. Save that change and restart Snort on the interface.
You do NOT need to be changing the HOME_NET nor EXTERNAL_NET variable settings. Changing those is almost never required. And changing them from the defaults without a full understanding of what they are for and how they work will result in a setup that will NOT trigger rules properly. The fact you altered them in an attempt to solve the problem you describe indicates you may not understand what those parameters are actually for. They define the networks to be protected (HOME_NET) and the networks that are assumed hostile (EXTERNAL_NET). The default setup puts every address/network not defined in HOME_NET in EXTERNAL_NET. Literally, in the PHP code, $EXTERNAL_NET is defined as !$HOME_NET (the leading '!' character indicates a logical NOT operation).
