Good questions. To answer the first one, if you switch from the Montgomery GI Bill to the new Post 9/11 GI Bill, you receive a refund of the $1,200 that you paid into the Montgomery GI Bill with your final housing stipend check when you use up the last month of benefits. If you never completely exhaust your benefits, you never get the refund.
As far as the second question goes, the short answer is that yes, you still get the college fund bonus on top of the new GI Bill benefits. The extra money you are talking about is the up to $950 per month that the services are authorized to offer to encourage enlistment in critical job fields. If you are due a college fund bonus (or “kicker”), it is added onto your housing allowance each month that you are in the GI Bill program taking courses.