Most rabbits hate to be picked up. In the wild they are prey animals, so it is natural to them to hate being picked up. Even rabbits that have a strong bond with their owners still hate being picked up. My Benji had a very close bond with me, yet that all when out the window when it came to picking him up. :roll:
My rabbit April used to be very similar, running away and thumping if anyone came near her, but with time she has got better. She still won't sit and let me stroke her or pick her up, but she doesn't run away as much anymore.
It sounds like your bunny isn't used to human company. You'll have to start with small steps, such as offering food out of your hand and waiting for them to take it. If you sit in the same room as your bunny and let him approach you rather than you approach him, that might help a bit. I would try and avoid picking him up as it sounds like it stresses him out a lot.
In answer to your second question, male rabbits shouldn't really be put together until they are neutered as the hormones can cause fights between them. It is strongly advised in most books I've read not to do so. Neutering should help, but even then it would take a while for the hormones to die down. Once they have both been neutered, there's no reason why they shouldn't get along really.