When it comes to hardware, I would really recommend you to look at a touch screen for navigation. It's gotten pretty good with MC. It's a lot of fun to browse everything by flicking through the media. Try it by flicking with a mouse to imagine how it will work.
I'm not a wizard when it comes to zones, but I do believe I would go for a two zone setup in your case. That way you could use two simple sound cards in combination with a surround receiver, and get independent music/video in the lounge and garden in stereo. But that's just me.
For controlling of the system I would go with a remote control for sure. I had a DiNovo Edge my self, but it was quickly replaced with a Gyration remote control. It has all the normal buttons and some MC specific, as well as a great gyro mouse control. You'll probably be using Theater View most of the time anyway, and the on screen keyboard functions is good enough to only have a backup keyboard laying around when you have to write or edit much. I'm using a Logitec DiNovo Mini as a keyboard and remote control sometimes as well. This one is SMALL and works great.
Remember that you could also use the remote ability of MC, and connect to your lounge PC and control MC directly through a notebook or similar low en PC. It could be used to control MC from the garden, when you don't want to put down that cold beer, just to change a song
IF you can do without the mouse control when using theater view, I'm sure you'd be very happy with the remote system J River is providing. As Jim said, it can control MC as well as other equipment via IR signal transmitters. It's a very affordable and thing that works with little problems. But remember that you can control the sound volume etc. on the PC it self, so it's not really necessary to control the volume in both places, unless you're using some other input as well. At least that is MY case.
When it comes to ripping, you CAN rip to wav. Some extreme audiophile people prefer that. I think it's a waste of space, and a lot of BS when they say they can hear the difference from wav and flac
Wav is a direct copy of the files, flack is a format for lossless music with compression. Everything built in in MC. You can activate the Flac plugin in the plugin manager, and select your ripping process to use this. You can sett the compression level at what ever you want. No matter what setting you select here, the music will be just as lossless! In tother words, the best quality. It's just a matter of how hard its compressed, and how good machine you'll have to have to code or decode it (it don't demand much anyway, but can take a bit longer time to rip).
