I've never used a Bowflex, but I do use a mix of free weights and machines at the gym.
Freeweights are better if you can use them. Like others said here, they work out secondary muscles and it does make a difference. However, if you are using very heavy free weights and don't have a spotter, then I would reccommend using machines. When I do my bench presses I use the machine (unless I have a spotter) just so I can go that extra rep. When you work out, you should work out to complete muscle failure... until you can't possibly do one more rep. I can't do this when I don't have a spotter and I'm using heavy free weights. There is a good chance that I mgiht not be able to finish the last rep and then kill myself.
Other good things that I reccommend:
You should set goals before going to the gym or working out. This will save time and give yourself a better workout. Some days you might not be able to lift as much because you are tired or whatever, but you should make an effort to go up a little each week. Even 1 more rep is an improvement from the week before, but I wouldn't go out of your rep range. Depending on your goals, you will want to have different rep ranges. For pure strength training, 1-3 reps per set is best. For body building, 8-12 is best. Anything more than that is strictly endurance training for the muscles. 3 or 4 sets is a good place to be for each exercise. Start with complex lifts (that work amny muscles) and finish your workout with single muscles workouts (so if you're doing back, bis, and lats in 1 day, start with lat pull downs and finish with bicep curls (use free weights for this, don't cheat, and don't use the preacher bench because you don't get a full range of motion with it)). If you can set your goals so that you're lifting enough weight so that you reach failure after 8-12 reps, then you're ina good spot. When you can do more than 12 reps, increase the weight.
If you are doing cardio, do it post workout, after a shake. Don't do it preworkout.
Studies have shown that muscles take 5-10 days to fully recover after working them out to exaustion. You're muscles aren't building during your workouts, they're building during rest periods. Too many people over work their muscles and wonder why they don't get results. Rest is very important and it's hard to do because a lot of complex lifts work many muscles, so you have to set your schedule up so that you get enough rest. I reccommend doing a muscle just once a week so you have 6 or 7 days rest.
In addition to those goals, decide whether you want to bulk or cut. When first starting out it will be easy to do both, but after a month or two you will have to pick one and then alternate. A few months of cutting and a few months of bulking. The reasons for this is the diets for each are very different. It is very hard to bulk while cutting fat and it's very hard to cut fat while trying to bulk. There is a middle ground, but the results will come very slow. After 6 months you will have much better results if you alternate between bulking and cutting than if you just kept a middle ground (maintenance). The main difference are the diets. Pretty much everything should be the same, but when bulking you should eat much more carbs (try to keep it under 1g per lb a day when cutting). Add more carbs for more calories when bulking and you'll see results (obviously, you'll need to burn mroe calories than you take in to cut, and you'll want to take in more calories than you burn to bulk. This can gain a little excess fat, but that's what the cutting periods are for).
While cutting, be sure to do refeeds every 4 or 5 days. Consider this a cheat day where you eat so many carbs that you can't burn them all. This is very important while cutting because it will raise leptin (and refill muscle glycogen) and prevent ketosis (starvation mode). When your body isn't getting enough calories and carbs while cutting, it will think it's starving. When leptin levels are low, ketosis will set in and this will actually burn muscle in addition to fat. Needless to say, your metabolism will be shot during this period. Refeeding every 4-5 days will prevent this and keep your metabolism and leptin levels at good amounts. This is the reason why people notice that they actually lost weight a day or two after they cheated on a diet. The atkins diet is pretty dangerous and I don't reccommend it.
More important than the actual working out is the diet. If you are lifting, be sure to get at least 1 gram of protein for every pound in your body (the more the better). This should be spread throughout the day, but this protein is especially important pre and post workout. Pre workout meals should consist of slow buring proteins if you are eating an hour to 30 mins before working out. No carbs pre-workout. Fast burining protein (like shakes) should be used if you're having your preworkout meal right before lifting. Your post wokrout meal should be done as soon as possible once you finish working out, and should include fast burning proteins (shakes) and carbs (try not to have sucrose). Muscle building starts immediately after you finish lifting, so get those proteins and carbs in your body as soon as possible.
Be sure to space out your meals. 3 meals a day is not good for anything. There is too much time inbetween meals and it causes your metabolism to drop. Have 5 or 6 smaller meals throughout the day and it will keep your metabolism high. You will burn more fat this way and there are constant nutrients going into your body insteady of bursts of it. This is a very tough system to get used to. Be sure to have slow buring protein before bed. Try not to have too many carbs at this time. This will keep your metabolism up while you sleep.
Alcohol is the worst thing. It's the only calorie that your body can't use, and it actally hurts the muscle growth process. That's not to say to stop drinking occasionally, but alcohol is not good for you.
Be sure to take a multivitamin and have enough vegetables in your diet. Try to drink a gallon of water a day. Don't eat candy or useless stuff like that. It's tough at first but after a while you feel so good eating "good food" that even thinking of eating candy will make you sick.
even just benching .