That's a great choice for a finish! Aqua Coat is a fantastic product and very user-friendly.
It's the prep work that's crucial to a smooth finish, so make sure your piece is sanded to at least 220 grit and dust free.
I'd definitely recommend using a tack cloth to get every last particle.
Then when you apply the Aqua Coat, go for several thin coats instead of one thick one.
It levels out really nicely and you'll avoid drips and runs.
Sand lightly with 400 or 600 grit between coats after it's fully dry, just to knock down any dust nibs.
Just be careful no to press too hard, you're only scuffing the surface.
Then for the final coat, you can skip the sanding!