Deformity is a common side-effect in panorama-stitching. It happens because you're trying to make a big flat picture from a variety of photos which were taken while rotating yourself (or your tripod). In addition, all lenses have some distortion, which makes the photos harder to match up.
One way to fix up deformity is to add markers for horizontal or vertical lines in your photos -- for example, put a line on the horizon and label that as horizontal, which will force it to be straightened out. I don't know how to make your tools do that in particular, but it is a common feature.
In addition, when picking corresponding points on two different photos, try not to pick points near the edges of the photos. That's where a lot of the distortion occurs, and it can confuse the stitcher and make for poorer results.
Finally, pick a lot of points, spread around the photo (not too near to the edge). Pick points in the upper and lower parts, and on the left and right. That will give the stitcher more data to work with.