You need to define two separate services, or to override 'db' service in a way that will accept your custom parameters or flags in order to distinguish between two RDBMS.
One thing is for sure, go for pdo_dblib
/ FreeTDS to work with MSSQL. Phalcon does not support MSSQL as native adapter, so you'll need to either use PHP PDO or to build your own set of classes / methods (ORM) to work with it.