The nice thing about CorrosionX is you can clean the board with Contact Cleaner and easily do repairs. If you coat with a more permanent coating such as the silicon stuff, you may run into some complications for any repairs you may need to do in the future.
To answer the question about how to use the CorrosionX, as RJ also stated; just lightly spray both sides of the completed board. Nothing needs to be protected from the spray, just do it. It does not dry hard and can easily be cleaned off with contact cleaner if you need to.
Spray it and forget it! It has the characteristics of penetrating oil and will seep into the tiniest places to displace water and prevent moister and water intrusion. Also, it does not last forever and may require annual refreshing.