Running them inside of the tower gives the best look. You drill holes in the tower and use either a rubber grommet or silicone to keep the wires from getting cut on the holes edges. (this will happen over time if you don't and when it does it will short the amp and probably fry it).
For cabling tower speakers, I use this: http://www.4electronicwarehouse.com/products/monster/cp14-4.html
I use neutrik speakon connectors for connecting it all together. The NL2FC for the tower wires and the NL2MP mount in the speakers. The NL4FC with the NL4MP for the mount for connecting the wires through the hull.
Here's a link to the NL4FC, the others at the bottom of the page: http://www.partsexpress.com/pe/showdetl.cfm?&Partnumber=092-050
I mount through the hull in case the tower ever has to come off this is all quick disconnects. You can also drill throught the base or foot of the tower and pass the wiring through the hole that way.