Flood insurance covers the cost from the water line down. Wind insurance covers from the water line up. If you're unclear of the what exactly is covered the best advice I can give to you is refer to your current policies. Wind and flood are two different policies. They require two different claims.
Here are some helpful links.
My name is Ray. I specialize in damage to properties. As a Florida State licensed Public Adjuster experienced handling insurance claims from low thousands to complete policy limit payouts, with a wide range of claim types from flood damage, fires, storms, wind, water, accidents, just to name some. Also, I'm a Florida licensed Building Contractor, I've been involved in repairs of condo units, single family homes, buildings, and businesses. My knowledge enables me to also inspect properties and how it's damages are related to policy coverages to provide appropriate estimates to consumers, lawyers, and other contractors. My mission is to do it right!