Please Note:
To update existing databases to 5.6.3.1, follow the existing upgrade procedures, i.e: any database pre 5.5.1.1 needs to be upgraded to 5.5.1.1 FIRST, then upgrade as normal to 5.6.3.1

To create a new database for a new customer, create a database through SQL Server Management Studio and then run the script file in NewDatabase_5_6_3_1.zip
This will create an empty database that is ready for use with build 5.6.3.1
You can then run the Framework and set up the site as normal

The Missing Indexes script will create ALL the indexes that we normally use. You don't normally have to run this, but you may give it a go if you suspect that some indexes are missing after the upgrade.