Yes they need different cages, and they have to have a few inches of space between the bars of each cage so they cant fight through the bars. My bonding pen was 3x4 divided in two, so two 3x2 cages with 3 inches between the two. This is not my current setup though. In my opinion a hutch divided in two is not enough room.
It depends on the buns and time you put into bonding, there is no set answer for how long it will take. Most let the buns get used to each other for a while before even starting the bonding process, I think I waited about a month, switching them in the cages daily and letting them get used to the others smell. My first bond toke maybe 3 months, but I was not as committed as I should have been because I was scared somewhat to move on, but that bond never actually worked, she died before it was over. My second toke maybe 2 months, but that was with daily sessions, sometimes several sessions a day and for hours at a time for the second month. Some take longer, maybe 6 months, sometimes never.
This is a huge commitment, so my suggestion before you get any more excited or involved is to read several bonding stories on this site and a few bonding articles. You need to know everything BEFORE you jump into this so you know for sure if you can handle it or not. Honestly, my first bond was horrible and I did want to give up because it is very stressful on the buns and yourself. Be honest with yourself and really think about whats best for you and your bun, its harder then it seems. Here are my bonding threads, id read them and others in the bonding forum.
This one is about Hammer's dating process http://www.binkybunny.com/FORUM/tab...fault.aspx
This one is the first bond I did http://www.binkybunny.com/FORUM/tab...fault.aspx
This is the second bond http://www.binkybunny.com/FORUM/tab...fault.aspx