A CRJ200 First Officer experienced confusion while attempting to reprogram the FMC to reflect a runway change. The downwind leg of the arrival remains on the south side of the airport which does not appear correct to the reporter and delays execution of the changes; resulting in a minor track deviation. Fatigue was cited as a factor in the incident.

Narrative

When we checked in with Atlanta Approach; we were assigned 26R. That caused a bit of a rush in approach set up and briefing; as we were expecting 27L because we were on CANUK 1 arrival. I loaded the 26R approach in the FMS. I ran through the legs page to review the changes; I got confused because the downwind in the legs page was still for the south side. To troubleshoot; I reselected the arrival. I did realize that this would load the arrival from the beginning; so I changed the first fix to the fix we were going to at the time; CANUK. Despite the attempt to fix the downwind problem; it still did not change to the north runway downwind. Then the Captain pointed out that the downwind did not change; because we did not need to fly the downwind as we were going to land west. I was happy with the situation at this point and ready to execute the change. I executed; with the Captain's concurrence. While I was confused about the downwind fixes on the legs page; we were already on top of CANUK. The aircraft started a turn to the left to go back to CANUK; which was already behind us when I executed the change. I realized that something was not right. I said 'where is this thing going'. The Captain then took the controls; disconnected the autopilot; and manually flew the aircraft back on course. We were less than a mile from CANUK; when we realized what was happening and took the corrective action. We were never more than half a dot off course during the whole event. No separation to my knowledge occurred. On the outbound flight; we had a FLAP FAIL caution message after the pushback. We had to return to the gate to let the maintenance troubleshoot. The troubleshooting process caused approximately an hour and a half of delay. By the time we got to the layover; we had five hours and sixteen minutes on the ground. With the van ride there taking twenty minutes each way; I effectively slept 3 1/2 hours that day. The whole flight to ATL; I was feeling the effects of sleep deprivation. So when I was confused by the downwind legs; my positional awareness got lost faster than usual. If I had more sleep; I probably would have realized that I didn't need the downwind legs. Also; I didn't check the first waypoint one last time before executing. Even though both the Captain and I checked the waypoints before executing; we flew over CANUK during the time spent confused about the downwind.