Yes, it is better to address the orange peel before clear coating instead of hoping the clear smooths it out.
All you need to do is sand out the orange peel before clearing. (You can polish the clear afterwards.)
Without any photos I can only give some general direction/advice. I'd say sand it with 1200 wet paper, check your progress often. You just want to take off the peaks of the orange peel so it is a uniform sheen with no spots (low points).
That grit will also leave enough "tooth" for the clear to adhere to.
The biggest concern is to not sand through the color. Be especially careful around the edges and high points of the parts. If you do sand through, touch it up. Once you have a uniform color base, apply the clear.
The next step is to learn how to apply paint with less orange peel...