Have a flight tomorrow from PHL to DOHA to MLE. Flight is American Airlines ticketed and flying American hardware to DOHA but QATAR hardware from DOHA to MLE. Checked in on American online with no problem. Qatar airlines checkin gave me a confirmation pass and no boarding pass and says I need to check in at counter 90 mins prior to flight. I have a long (9 hour) layover in DOHA and have room reserved at the airport hotel Oryx. A couple quick questions:
1. Will my checked luggage be checked all the way through to MLE or will I have to pick up in DOHA? I assumed all the way to MLE.
2. I was planning on staying in airport (not having to claim luggage). If I have to claim luggage and recheck before I fly to MLE, will I have problems getting back through security with luggage intended to be checked? I.e. we will have liquids and stuff in the checked bags.
3. Should I worry about the confirmation pass versus boarding pass? Can I do the check in for boarding pass inside security or will I have to leave hotel, exit security and check bag/get boarding pass and re-enter?

Thanks for the help.
-Bob