Yes, you will need to remove the soft top, and frame when you wish to put the hard top back on.
The assembly instructions that came with my Supertop were very good, and there are a couple of instructional videos that you can find with Google. You will attach the windshield header to the top of the windshield frame with brackets that are included and use the hard top latch slots. There are brackets into which the front frame of the top will seat that you will bolt into the front window frame using one of the Torx bolts that attaches the roll bar extenstions. The rear top frame attaches to the tub using the same bolt holes that are used for your hard top. Lastly, you will mount the two brackets on the rear tub rail that are used to tuck the bottom of the rear window in, these brackets also act as the tailgate bar retainer that helps keep the rear window firmly seated.
Once that is done, you'll be ready to get the top on. Read the instructions carefully and follow them, and know it gets easier once you have done it a time or two. Oh, and pay attention to the recommendations regarding the ambient temperature when you install the top. If it is cold, the top won't stretch as much, and you will have a harder time with the install......taking the top inside a heated area (garage, house) can help.
Hope this helps!