ok first off, the sound issue is almost always better if you go custom. I personally went with the factory system, but only because of the lack of cash to purchase all of the components to complete the install. If you go completely custom you have far more control over how the sound gets to the speakers and ultimately you can tweak the crap out of it for your specific vehicle. That being said, the easiest is to use the factory system with an aux in to get setup quickly. the advantage here is that the manufacture has done most of the work for you.
as far as controlling the music from outside of the car while at a show or something, you can download the itunes remote for the ipod touch, and the use that over an ad-hoc network in your car. to do that just go into your mini, right click on the wifi icon up in the top left menu bar. then select "create network" it will ask you for a name for the network, and will probably put a default name in there for you. it is perfectly fine to use the default settings (it will prob be something like "your-name-computer" or something like that). once you select "ok" the mini will set up a wireless network that you can connect to from the iphone/touch. just go to the wifi settings and select the name that you just entered in the mini. from there you should be good to go. on that note there is an awesome app called remote pad that is free for the iphone/touch that lets you turn the iphone/touch into a full featured mouse/keyboard for the mini. just install the helper app on the mini, setup the network as just described, and fire up remote pad and you are good to go.
if you have any other questions feel free to ask.
Good luck with the install!