Here is a picture of my (bookshelf style) desk, basically I pulled the monitors out as far as possible and then put traps in the corners. It looks really ugly in this picture, but actually without the spotlight on it for a photo showing the stuff, the directional lighting above mixed with black shelves really hides this. Also the panels are thick and heavy, very heavy. Mass helps keep resonances under control, so if your using particle board or light shelves, add some weight to them with books to keep them from resonating.
Those are ugly traps, but, you can get some nicer looking ones or be a bit more creative (I'm not married so I get away with the cheap but functional route haha)
Cable length differences won't matter. Nice thing with bookshelves is you can play with placement versus aesthetics pretty easy and come up with a happy medium.
Keep the speakers tweeters as close to ear level as possible.