Connor,
You are correct - pathing is a PAIN in WindRiver. We did, however, come up with a full fledged solution early last season. It is documented in:
https://github.com/bobwolff68/FRCTea.../windriver.txt
The trick is to use the WS_ROOT_DIR variable. See lines #45-#47 in that file specifically. But the whole thing may be found as a good read. That's our formula around much of it outside of the final output file being copied to a single hardwired location ALWAYS post-build. This makes it so the FIRST->Download plugin can be set to that location and never changed. Regardless of switching projects you'll always have the most recently built binary output in the right location ready to be downloaded.
Hope this helps.
bob