@rowe

You can set the destination path for your FGDB using a published parameter in the work space. However you will need to first get the path from your spreadsheet (in a previous work space).

If you are using FME server you can use the FMEServerJobSubmitter trasnfor to call the second works pace (with the destination path) or if you are running it locally you can use the WorkspaceRunner transformer to call the second work space.