When I installed the hard drive in my WRX my original plan was to drill a hole in the side of the glove box to run the USB and mount it to the top of the glove box with Velcro. But since my head unit is single DIN and I have a pocket above the head unit I ended up just mounting the hard drive in there because it was so easy and fit perfectly.
You can pretty much run it anywhere you want, but since it's for an iPhone I'm guessing you're going to mount the phone somewhere that it will be easily accessible, and I would run the cable to come out close to where you're planning on mounting it. If you're mounting your phone where will it be?
I don't know about articles for running cables.. I'm willing to bet Crutchfield has something of that sort. I could probably answer any questions you have.
One thing that often gets overlooked is; when installing your new head unit it is preferable to ground it directly to the chassis somewhere in the dash rather than running it through the ground in the factory harness. Who knows how long that ground wire is, and it runs side by side with all kinds of other wires.