Have you tried the SQLSample1 project?
I made these small changes to the sample and it creates and opens 2 SQL DB’s.
var DB; //the database itself
var DB2; //the second database
Then in the initDB() function:
DB = SqlOpenDatabase("customer.db", "1.0", "My Customer Database");
DB2 = SqlOpenDatabase("information.db", "1.0", "My Information Database");
When I inspect in Chrome, they are both created no problem. Once you create the two DB’s you can then create whatever tables and queries you want in each of them.
This is not a complete solution, but if you follow the code in the references example, there is no reason why you can’t accomplish what you are asking.