Lightroom processes whichever photo you select. You can process both differently if you like. Remember Lightroom does not change the original it just saves the changes it made to the original. If you have a choice you should always work with the RAW file because JPEG files are heavily modified already and you will get better results using the RAW file.
When I load the photos from the file it only loads one, and I can't tell which one it is. I would suspect the default would be to choose the raw format, but I don't know. I am tempted to change my setting to only take raw and not both raw and jpg in my camera. Of course when not in manual, I don't have a choice but to get jpg format, as far as I know.