CRJ200 FLT CREW WAS ISSUED A RWY CHANGE NAVIGATING THE FLCON RNAV ARR INTO ATL. THE FLT CREW CHANGED THE FMS FOR THE TRANSITION APPROPRIATE TO THE RWY CHANGE. ATC'S INTENTION WAS FOR THE FLT CREW TO REMAIN ON THE ORIGINAL TRANSITION.

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INBOUND TO ATL ON THE FLCON 3 ARR WE WERE TOLD EXPECT RWY 8L WHICH IS A N SIDE DOWNWIND. PASSING BY WORFF INTXN WE WERE TOLD TO CHANGE RWY TO 9R. ON THE FLCON 3 ARR THAT TURNS YOU TOWARD BOJAA INTXN AND A S SIDE DOWNWIND. WE COMPLETED THE FMS CHANGE AND TURNED TOWARD BOJAA INTXN AT 11000 FT. APCH CTL THEN TOLD US TO DSND TO 7000 FT. THINKING THIS WAS A MISTAKE WE QUESTIONED THE DSCNT TO 7000 FT. SHE THEN ASKED WHERE WE WERE GOING. WE TOLD HER BOJAA INTXN PER THE FLCON 3 AS ASSIGNED. SHE THEN CAME BACK WITH STOP YOUR DSCNT AT 8000 FT AND MAKE A HARD R TURN TO DIRECT NOFIV INTXN. SHE THEN CHANGED THE INSTRUCTIONS TO EXPECT RADAR VECTORS TO RWY 9R. SHE THEN STARTED REPEATING THE RADAR VECTOR INSTRUCTIONS TO THE ACFT BEHIND US. WE WERE NOW ON A N SIDE DOWNWIND TO RWY 9R UNDER RADAR VECTORS AND OFF THE FLCON 3 ARR. THE REST OF THE ARR WAS NORMAL. THE PROBLEM OCCURRED WITH THE LAST MINUTE CHANGE TO RWY 9R AND NOT BEING REMOVED FROM THE FLCON 3 ARR. THE ARR ON PAPER NOR THE FMS GIVE YOU THE OPTION OF A N SIDE DOWNWIND TO RWY 9R. I FOR ONE WILL QUESTION WHICH DOWNWIND THE CTLR WANTS WHEN THERE IS A LAST MINUTE CHANGE IN RWY ASSIGNMENTS AT ATL.