In the right part at the bottom ( PDF Editor for JIRA Panel) you can change the files order using the Up and Down arrows and choose the files to be exported using Select / Unselect action

Once you have selected and ordered your files, you can start the export using the Export Action, please see below: 

The "Export" Action will combine all selected attachements in the order you specified into one single PDF file which will then be attached to the Jira issue.