From Wes, the big show at ironaddicts.com.
Here is why running and weightlifting are NOT compatible. A 200 lb guy produces between 800-1000 lbs of force on every foot-fall when running. It is not a big deal until you add up the 1000's of impacts during a jogging session. It dampens CNS output. CNS IS what allows you to lift the weights. Dampen CNS to any decent degree and you will find you cannot progress with the weights. It produces a lot of cortisol. Cortisol slows or halts muscle growth once too much is present. Because of the eccentric component protein turnover goes up. You end up protein deficient even though you are consuming a lot. The body has inherent intelligence. Running and lifting heavy objects are at opposite ends of the spectrum. First you try telling your body it needs to increase mass density by lifting heavy things. Then you run which tells the body that being lighter is an advantage. You end up short circuiting the growth process. Try and find BODYBUILDERS--not guys that lift weights that run. You will find VERY, VERY FEW, and if you do find an example, what you are really finding is a genetic freak often on steroids. If that is not you, you should consider leaving out running. IA
Short version: if you suck at both, sure, do it. If you are doing one or the other seriously, pick one. edit: it sounds like you want to have your cake and eat it too. 4 days of upper body workouts / week, want to gain all muscle and no fat? get your head outta the clouds, son.. be realistic. Either get used to bulking/cutting if you want to get big, or research ketogenic diets if you're interested in maintaining mass while cutting fat.