Hello Micchael,
First, there is a very good blog series by Colin Maitland which covers the Instance Adapter quite well. You'll have to work through to the older posts, but I think you'll find it well worth the effort. www.magnetismsolutions.co.nz/.../colin.aspx
As for getting all of the data for each map, you will want to set the "check for data modified after" in order to pull the data that is already in the instance. Connector uses a polling mechanism on modified date to determine net-changes. By changing that to a historical date - say 1/1/1900 - you should get all of the data to come over.
Cheers,
Jeff