First off, be sure not to overwork your muscles by over training them. Many people see what a lot these big time professional weightlifters are doing and think they can get the gains they are making, but in reality they are genetic freaks and a majority of the time are taking steroids.
If you are going to workout twice in one day then it is best to devote one workout to cardio and stretching and then the other workout devote to weight training (probably not wise to even train legs and run for long periods on the same day). It all depends on what your goals are. If you are looking to lose weight then run in the morning right after you wake up and weight train at night. Otherwise it doesn't matter too much which you do first.