I love it when people say "I don't want to be a bodybuilder" as if becoming one were something inevitable that requires no effort, like developing hemorroids or something.
I guess everybody covered it up, so I'll just parrot my way.
1. Free weights. There is a time and place for machines, but more often than not they have no place for people starting up. The only time for machines is as supplements (not replacements) to training with free weights, or in case of rehab for injuries.
2. There is no such thing as 'toning'. You develop muscle or you don't. You loose body fat and become lean, or you do not. Your ability to loose body fat is directly related to the amount of muscle you develop.
3. To go from "doughy to some muscle" you need dedication, almost the same dedication as in bodybuilding. What make people into bodybuilders are their nutritional choices and selection of training methods.
4. Drop the cardio. Forget about cardio. You don't have sufficient muscles to benefit from cardio as a fat loss mechanism (you realize this already so that's good.)
5. Get Mark Rippetoe's "Starting Strenght 2nd Edition". Also check Oxygen Magazine and pay attention to the workouts and recipes. I prefer this magazine over male-oriented fitness/bodybuilding magazines. The stuff in it IMO is much superior quality and applicability.
6. Do high intensity interval training, first once a week and later twice a week, preferably on days when you are not lifting... in addition to weight training. Search for HIIT, "hight intensity interval training", "interval training" and "tabata". 5-10 minutes of it >>>> 30-40 minutes of "cardio".
Observe the following clips to completion - don't skip any video. Watch them all!!!
Introduction to HIIT
HIIT on a stationary bike
10 minute HIIT/tabata workout
Tabata Squats (20 seconds, as many reps as possible, 10 secs rest, for 4 minutes)
Good luck.