You are supposed to use the Scheduling as is part of Tableau Server. Going any other way is actually the alternative Folks who can Publish will select the schedule and either full or incremental extract. The Tableau Server admin can manually do this as well if necessary.
Packaged workbooks can be refreshed just like an extract and without any performance penalty --> http://community.tableau.com/thread/132128
Thanks for responding. The issue we're having is that if the source data is delayed, the Tableau workbook refreshes before the data is ready. If we could connect the refresh to the source data being ready, then we can be sure of a good refresh.
Also, the refreshextracts workbook-name is only tabcmd, which we can't do.
We're going to convert our twbx files to data sources, so we can do the command line refreshes.