Ok, you can add a keypad within your media room to control the multi way master at bottom of stairs if you want to keep the IR. if I were commissioned to install a system there, I would install Radio Ra2, however you can't install that yourself.
I recommend you using the maestro wireless version. If you have 2 multiway, and 2 companion dimmers then I would get 2 pico wireless remotes, and maybe even the little 2 remote base to make it more convenient.http://www.lutron.com/TechnicalDocum...y/0301281A.pdfhttp://www.lutron.com/TechnicalDocum...ry/369-143.pdfhttp://www.lutron.com/TechnicalDocum...0Submittal.pdf
Based on your (2) locations of 3-way circuits, you need the following:
(2) MRF2-6ND-120-XX dimmers. The "XX" is color, and I'm assuming you are ONLY using incandescent ( NO CFL's ), and it's not de-rated over the limits and not over 600 watts. Your father in law will know this info if he is an electrician
(2) MA-R-XX companion dimmers. These are what the "old school" electricians called the slave switch before we all went PC.
(2) MRF2-3BRL-L pico remotes. You can use 1, but it will control both zones together. You will want separate control
(1) L-PED-XX This is the little pedestal for the pico remotes. You can also wall mount the picos like normal switches which is cool if you need a switch where there isn't one.
This will get you what you want, and it's all RF, no line of sight. And NO, don't ask about integrating with an RF Harmony remote. There is an option with URC I believe, but that's for another topic.