You need to make every section of your map LIGHT BLUE, even the sections you don't know are there just by looking at your map. Still, it's best to go ahead and fill in every place as you go along. It encourages you to explore a great game.
Before the final boss fight, make sure you get anything you may have missed. I tried to fill up everything on the maps, and I was at 200.5% before going in to the final fight.
You can check your progress at any time by going from the main menu to your save file in-game.
Compare your map with these maps: http://www.execulink.com/~maggi/wbw/2006.html
They need to look the same. If it helps, the last square I found to hit 200.5% was X=106, Y=47.
If you need help getting to a certain area, try this great walkthrough:http://shrines.rpgclassics.com/psx/castlevsn/walkthrough.sht...Hidden Rooms
Inverted Castle Hidden Rooms
To fill in the areas in the water, you'll need the Holy Symbol so that you can traverse the water without taking damage. This allows you to morph into the wolf while in the water so you can swim (Y) and reach the areas you need.How to get the Holy Symbol
How to fill in the final gaps
I take no credit for the videos, walkthrough, or maps.