Hi I am trying to understand how to use tap-mssql. How do I specify the sql to use or table to extract from a database?

You can't specify the SQL that's used - the tap generates that itself. The list of tables to be extracted is controlled by the

select

rules in your meltano.cfg though.

May I also offer this little mssql example in case it's useful: https://meltano.slack.com/archives/C01TCRBBJD7/p1686300057741609?thread_ts=1686135925.112829&cid=C01TCRBBJD7