Two db connect files

For one thing, you don't need separate database connections to the same server. Simply specify the database name before each table name in your SQL statements. For example:

SELECT foo, bar FROM db.table;

rather than:

SELECT foo, bar FROM table;

For another, you shouldn't be storing the database connection in a global for just the sort of reason you're running into. I suspect you're using the outdated mysql extension, which uses an implicit DB connection resource whenever one isn't explicit. Switch to PDO and create a simple connection manager class. One big advantage to PDO is it supports prepared statements, which can be safer and more performant than what the mysql extension provides. If you need a PDO tutorial, try "Writing MySQL Scripts with PHP and PDO"

If it is a separate db server you might need to look into the mysql federated engine which allows you to link to databases on separate servers as if they were on the same host.