Bathtub drain system

We are in the process of replacing a garden tub with a one-piece tub/shower unit. We have replaced flooring, ran new water and drain lines and have the tub leveled and set into place. We cannot get the drain stopper to seat properly into the drain opening and still have the drain line run at a slight angle to allow water to flow freely. Any suggestions? Any comments about the most common problem unskilled plumbers might face during this portion of installing a bathtub? No idea what problem might come up next but we are really stuck at this point.