It takes some practice to make good stacks if you’re doing it handheld. Helicon is good software and will work with misaligned images to a point. There are settings you can tweak (See Helicon forums / user groups) to accommodate greater degrees of movement, but at some point the camera has moved too much between shots (and thus the perspective changed) to be able to create a workable stack.
Helicon has a 30-day free trial, so you can keep all your source images for awhile, then run them all through the software once you activate the trial. This will give you an idea of whether it will work for you.