I went to my local shelter to go find Bambam (6 month old altered male) a mate, when I got there, there was only a 6 week old baby female bunny and i fell in love and brought her home. I do know she is supposed to be altered but I will get her neutered as soon as she is old enough!

When Bambam saw the girl he first sniffed her and was hesitant and she just sat and let him do what he wanted to. Everything was going well until Bambam growled at her and lunged for her, i managed to intercept when this happened and no harm was caused. I am a first time bunny owner and now have no idea what to do, I have put the girl in another room for the time being.

Please help, I would really like this to go smoothly! 

Sometimes when introducing a very young bunny, the older bun will be fine with them for the time being. In this case, it sounds like you will need to absolutely wait until after she's altered to continue with bonding. You don't want one or both to get injured. It does appear that it's going to be a more difficult bond, but it's by no means impossible.

Do you have any suggestions to keep them civil in the mean time? Bambam is perfectly fine when she is not near him and flops around my room when she has been taken away. I have tried taking some of her droppings and leave them in his litter box and put some food that she has taken a few bites from, in his cage and he refuses to go near them.

I woud keep them seperat untill she is fixed, even thier habitats. and try to reintroduce them in a neutral area after she is healed from being spayed.

I would keep them separated entirely until you're ready to begin bonding. Is there a different area she can be in that is away from him? You will probably have better luck introducing her as a "new rabbit" after she's spayed.

Update:
I have put the girl in a cage and bambam is running free in my room (as per usual). when I put the cage in my room, Bambam goes near the cage, sniffs and binkys in the opposite direction, then other times he goes near and growls at her and growls at me when i touch him to pull him away.
What does this mean??
Sorry - never done this before - bit of a paranoid mom!

I agree with Beka - I would separate them completely so that once she's spayed, he'll think she's a completely new bunny (spaying will also change her scent, which will help).

If you absolutely have to keep them in the same room and want them to get used to each other, you could try buying two stuffed animals and giving one to each bunny, then switching the stuffies every few days so they can get used to each other's scents. You can also swap cages every few days.

You really can't tell anything by how they act through cage bars. Many bunnies are very territorial in those situations, but it doesn't mean all that much about how they will be during bonding.