There are trades to be made between both choices, and the answer can vary between installations. Either choice can be made to work well. I prefer very short speaker connections with the amplifier a few inches from the speaker. For multichannel this generally means some relatively long inteconnects, which may need to be balanced if you are in an electrically noisy environment. I want to try wireless digital interconnections in my next upgrade.

Put me in the short IC and long cable column. Some cables can easily make for longer runs without problems. If I did have to run long cables, I would make sure to get them up off the carpet.