Regarding creating a mapping table, you will need to do that in SQL Server.
Create a database, and add a table that contains columns for the Source Guid and Target Guid and unique identifiers.
You can also add another field to your System User entity in CRM directly called Target System User Id (Single Line of Text), and store the Id of the CRM Online user record there.
Regardless of which one, in SSIS, you would create a lookup component that would query SQL and retrieve the fields of both entities.
For the lookup control:
In the General Page you need to specify how to handle rows with no matching entries: Ignore, Fail or Redirect to No Match or Error Output.
In the Connection Page, specify your OLE DB connection and the query. You query will be something like this:
FOR CRM: SELECT SystemUserId, new_TargetSystemUserId FROM FilteredSystemUser
OR
FOR SQL: SELECT SourceUserId, TargetUserId FROM UserMappingTable
In the Columns Page drag the Owner Id/Created By field to the Source User Id field, and check the Target User Id field
In the Error Output Page, select what you want to do with Errors and Truncation: Ignore, Fail or Redirect
From the Lookup Component you can continue to your Destination Component
If your Source data has multiple User Guids that need to be migrated, you will need a lookup for each.
There are a lot of example online. Search for SSIS Lookup Control.
Hope this helps you out.