If you're still using the Arduino IDE to compile your sketch, the 2nd last line of output before the "binary sketch size..." will tell you where the .cpp.hex file is created. Something like this:
Copy and paste that path into Xloader, and you're ready to upload.
I find this very handy for sharing a hex file with others working on a project who do not have the IDE loaded too. Make sure they have Xloader, and all I need do is drop the latest hex in dropbox.
I'm pretty sure AVRdude is what you'd need to use, but I'm not proficient in its standalone use but here's a tutorial from Adafruit that seems to cover a fair bit of what you're looking for I think.