Hi Sean,
You can still use the remote systems explorer to copy your program from your host machine to the target file system. You don't need a linux host OS to do this. But you will need an ethernet connection with your BBB. Using the remote systems explorer is shown in section 3 of the document you referenced.
The Linux Debug training module also shows an example of the remote systems explorer (starting at slide 44)
http://processors.wiki.ti.com/index.php/CCS_Modules_Library#Linux_Debug
Thanks
ki