Thanks for your post.
I'm afraid I'm not familiar at all with the Wherescape tool you mention, although that's probably not too relevant.
To source control data (with SQL Source Control) the data must have a primary key or a unique index. If neither of those are present, then our data comparison engine doesn't know how to evaluate which records should be compared.
The SQL Data Compare tool allows you to configure a "custom comparison key" where you can manually select one or more columns that, in combination, would uniquely identify rows. Unfortunately this functionality isn't in SQL Source Control as it stands.
SQL Data Compare can compare from a database to a set of scripts, so potentially you could sync the DB to some .sql files after configuring a comparison key and then manually source-control those files using something like Tortoise (if using SVN) for example.
Some links that give more detail:
What is a comparison key?
Selecting a comparison key