pick two muscle groups a day. one big muscle group (chest, shoulders, back) and one smaller group (bis, tris, lats). legs are their own day. do 4 exercises for each body part, and for each exercise do 4 sets of ten. minute rests in between each set. preferably increase the weight in between each set. the last set should be the hardest.
if you are overweight go for that 3 mile run. if you are lean but not muscular, don't run THAT much. you should definitely run, but it'd be better to be playing a sport. long distance running burns fat AND muscle, that's why cross country runners are not muscular. sprints and most sports drills (since they are usually brief with break in between) help your endurance without burning muscle, that's why olympic sprinters are jacked, even their upper body. that being said, get into sports if you aren't already, otherwise use running just as a 5-20 minute warm up for your work out.
drink lots of water, eat protein, maintain a balanced diet. if you want, buy some whey protein and drink shakes once a day. most of all, enjoy yourself. working out can actually become something you enjoy rather than despise.
ALSO, when lifting, don't go for tons of weight. yeah you may get some looks from the ladies at the gym if you throw on those extra 20 pounds for your bench press, but it alters your form and in the long run hurts you more. find a trainer and have them go over your form with you, because someone who really knows form can have their muscles burning after 5 reps of 40 pounds versus the 20 reps you were doing before with 70 pounds.