How to inject additional SQL Code into script

As part of the differences/upgrade script produced, at the end and within the same transaction we want to be able to call stored procedures and update data tables (e.g. update the internal records that contain our database schema version).

Of course we want this to happen as part of the same transaction.

Is this possible?

We currently use the SQL Compare tool and then modify the script to perform these actions, but of course this cannot be done if we automate this process.

Or is there some way to wrap the current code up so that it uses an external transaction, and we can then perform the actions using normal ADO.NET functionality.

Thanks,
Myles.