Oke, so you already have websites running on the new server, bad idea!
Now it just became a "merge" which is more work.
Better merge to the server which already has the most data (since the merge needs to be done manually in the ISPC3 webgui). Then you have one server with all data again which you can easily move to a new server again.
So create the users / sites / databases and everything through the ispconfig web interface and then copy / dump the data to each dir / database and set user permissions correctly.