I have a running "on" season and an "off" season. I use my off season to build up more muscle with programs like STS and more focused weight training. When I'm in my on season, I can maintain the definition, but I focus more of my energy on running and I lean out a bit. I don't think I would want to have too much muscle on me as I'm marathon training -- whether it's fat or muscle, you have to carry every pound for 26.2 miles.
Maybe someone else has a better answer on how to do both -- I just go in cycles...
Charlene