When compiling to OXCE+/bin/ and running from that directory, it should have the same folder structure as that in the Piratez download, and you can just copy over the folder structure of Piratez to OXCE+/bin/. Alternatively, you can just copy the executable from OXCE+/bin/ to the decompressed Piratez folder, wherever it is, and run from there.
With the New Battle, you really have to know what you're doing if you don't want it to crash - not all missions work with all terrains. In fact, I'd say most missions are tailor-made to the terrain/map on which they take place. Best to test with a regular campaign rather than using New Battle with Piratez.
Edit: The user and config folders default to ~/.local/share/openxcom/ and ~/.config/openxcom on Ubuntu for me, so I usually run the game with command line options to look in the same folder as my executable, to keep it all in the same place.