You will not be able to properly and permanently bond your rabbits until the male has been neutered. The first step in bonding is for both rabbits to be spayed or neutered. They might bond at first, since he is a baby, but as soon as he hits puberty and his hormones flood in, you will have to separate them, then wait until he has been neutered, plus a few weeks wait afterwards. So, instead of bonding them now, then having to separate them, it would be better to house him separately until after his surgery and recuperation time. He could be in the same room with your bunny, but not together. A bunny really should stay with his mother until he is 8 weeks old. If you are looking for a companion for your female, almost all rescues spay and neuter their rabbits, so if you got a male from a rescue, he would already be neutered, and if that had been done at least a few weeks before you adopted him, you would be able to start the bonding right away.
I find that the best way to bond rabbits is to put them in an x-pen, and you get in there with them. You can break up any fights and you can pet each one at the same time to hopefully calm them.