You may want to create a linked server, if you have a provider for SQLite that SQL Management StudioServer will accept.
Connect to your database and then navigate through "Server Objects", "Linked Servers" and add a new linked server. You can then use SQL Server to query the SQLite database, and compare the results directly.
Here is a tutorial for MySQL, so if you can create an ODBC connection for SQLite then you will be good to go.