I'm currently working on an RFID project for controlling an entry door and logging its status. I'm using the Innovations ID-12 RFID reader which uses Manchester encoding. Some of the other readers I've looked at used different means to communicate the ID code of the RFID tags. Before you getting too deep into a project, I recommend that you choose your reader first as his will determine the code you need to write and o some degree, the type of microcontroller you'll wish to use.
I'm more than happy to share my findings to date.
Regards,
Sherm