It's inevitable that you will have to sand out some runs, but here are a couple of thoughts on minimizing the amount of sanding needed.

First, a squeegee works well depositing epoxy into the low spots in the glass weave. This makes it ideal for applying a second coat. By the third coat the low spots should be mostly filled. A brush can be used to apply epoxy, and with care the runs can be minimized. A roller is also a good tool at this point. Rollers are very good at putting down a thin even film. Unfortunantly you're looking for a thick even film. So you might need several roller-applied coats. I've had good results applying epoxy with a roller and tipping it out with a foam brush to pop the bubbles.