Say they say do 3 sets of 12 reps does that mean that you do 12 reps then stop for a couple seconds and go do 12 again then break then 12? or is it that you do a set then leave to another machine then go back later until you do 3 sets... stupid questions but i just want to make sure

well, you dont only wait a few secs.. the time depends on your goals. for pure size its less than 2 minnutes, for strenght or end (?) its 3-5 minnutes.
say you do 12 reps of bench press, wait 3-5 minnutes then do 12 more reps then you have done 2 sets of 12 reps

Naw man this has always confused me. I will have it down packed, then confuse myself once again. Took me some time, but I got it down. Its the simply things that get me all mixed up. It happens.

If you are going to do 3 sets of 12 reps then yes, you will do 12 reps of an exercise, then rest, usually 10-45 seconds then do another set of 12, then rest agian then finish off your last set of 12 reps. Now depending on your work out that your doing, you can switch, say your doing chest and bi's on the same day, but instead of working out chest completely then bi's you alternate exercises. or you can even alternate Sets.
Each has its advantages.

Ok so say im doing my Biceps and pecs I would do this? with no breaks in between, thats one way though

12 reps of pulldown
12 reps of pec deck
12 reps of pulldown
12 reps of pec deck
12 reps of pulldown
12 reps of pec deck

then i just did 3 sets of 12 reps on each

You could do it like that, it's a little more hard.. What are your goals (this will determine how you should rest between exercises)? And please tell me you're not just working biceps and chest..

He's not, he is doing lats too

Not according to him
lol

haha yeah I got a kick out of that

Yes, you just did 3 sets 12 reps on each. In regards to what mreik said, you are doing more than just that right? you don't have to do several muscle groups in one day, and even if you are just doing one muscle group a day that is fine, again depending on your goals and how long you've been working out for. Each time you work out a muscle group, you should do 3-5 exercises just for that muscle group. And also to make it a little easier, i would focus on all the sets for one exercise before moving on to the next.

What are your goals? are you focusing on building muscle, endurance, increasing weight, lossing fat, ect?

oh no I just pulled that out of my ass, just as a example. My goal? I guess to get bigger muscles

In building muscle, try to focus on heavier weight at less reps. for example, on chest you might to 10 sets 3 reps increasing the weight each time, then move on to do incline, delcine, butterflies, ect. in a similar fashion. your last couple sets should be really hard, even if you can't get through the whole three reps and either do one rep at a time or stay at that weight for the last two sets. (after bench you could stick with 6 sets 6 reps still increasing weight though)
another workout that is very good for building is a pyramid workout, and i've seen this done several ways all with good results.
start out with a light weight and do about 15 reps, after each set you increase weight and decrease the amount of reps you do, each set will be difficult.
I've also seen where once you get down to your last set at 3 reps, you start to decrease weight and increase the reps.
Or at the end of your workout, you could also start at the heaviest weight and go for one rep, then decrease the weight and do 2 reps, then decease again and do four, then again and do 6 then again at 8, 10, 12, and 15.
if doing this as your last exersice, try it with no rest in between sets, if this is what your starting with, take 15 to 24 secs rest between each set.
Also, when maxing out like this, its best to have a spotter.