When I put my kids in teams they sit together all the time. I am lucky enough to have flat-topped desks that I pull together to make a small table. Teachers who have the L-shaped desks put their kids together, too, but they have to leave a little gap between the chairs to allow the kids to get in and out. View the Seating Options PDF file to see how to arrange these types of desks. If you have desks with slanted tops, sometimes you may want to have the kids move to a space on the floor when working on activities that require a flat space. I have tried to draw 2 of the arrangements I have used. I prefer what I call the T-Table now because that way no one has their back to me but the kids don't have eye-to-eye contact all the time. I would rather that they are facing the front of the room than facing each other all the time. When students are doing individual work, I have them put up "barriers." These can be pieces of folded cardboard or just their 3-ring binder notebooks. We've also found that 2 file folders placed end-to-end and laminated together make a nice barrier.
Some teachers leave their kids in rows at first but just seat the kids in each team close together. When they do a cooperative activity they have the kids pull their desks together for a short time or have the 2 kids in front turn around and use the 2 desks behind them. When they get more comfortable with CL, they let the kids sit together all the time.