Yes - best done through a Dock and simply run a cable from the dock line output to one of the Tape inputs. If it is a reasonably modern iPod, you can use the Apple remote to control it.
If you want to control your iPod through your B&O remote, you need to chat to Ridax and get one of his kits. It works with the 5000.
The S50 is a perfectly good small speaker - it just is not as good as the S45-2 which it and the S55 replaced. The S55 is a bit better though I still prefer the S45-2.