wifi problems with new access points

We just bought and deployed 2 cisco WAP561 access points. i set them up in single point mode for easier management, since we deployed these we have had horribly intermittent wifi, it will work great for clients then suddenly they switch to the other AP and loss all throughput sometimes it drops them all together and sometimes they stay connected with no network or internet access. Usually they have to turn their wifi completely off and back on again or reboot. I do remember when i did the single point setup it set them both the use the same channel but switch channels if it would increase the signal strength by 50%. the fact that are on the same channel is what I'm thinking the problem is, i though if AP's are on the same channel even on a roaming network with would create all kinds of havoc but I've heard the opposite and why would the AP's in single point mode automatically is the same channel if it would create problems. So the question i guess is, on a roaming network with the same ssid should the AP's be using the same channel or different ones? the APs are in range of each other, but with serious signal degradation in between.