JoshuaT,

You can refer below link on how to convert spreadsheet to new format.. This script will go in script task.

http://blog.quasarinc.com/ssis/save-as-a-new-excel-file-in-ssis-2012-script-task-using-visual-basic/

You can use variable to read the file name and check if filename has extension as .xls then execute above script task else skip this script task..