you actually do NOT want to fill all o the bays up. i would keep as many open as possible and keep the 120mm fans which are located there. this will be much better for airflow and will give your system lower temps.
going by the photos this gives you 3 slots to play with and the rest being used for fans. personally what i would do is have the cd/dvd in the top slot, the temperature gauge in the second and a fan rheobus in the third provided all are one slot high. if your temperature gauge is also a fan controller and is one slot high i would put a multi-card reader below it if you use sd cards or other formats or another cd/dvd above it if you do alot of disk burning. if you dont need a rheobus, second cd/dvd or multi card reader and only want something cool then get a lcd display and program it with a message, a lockable drawer or volume knob.
http://www.lifehacker.com.au/2012/04/five-useful-upgrades-for-your-computers-unused-bays/
definitely keep the bottom bays open though for airflow. dont block the fans.