There are a bunch of tricks for Psunami. You can use the image maps to displace the water and to lay the logo on the water. The displacement works fairly well to simulate a boat wake or a shoreline. The problem with using image maps as displacement is that they aren't flat. IOW, they follow the flow of the waves.
The key to making Psunami work well is to make sure that you pick Realistic or better for the Render mode, and when working with image maps to displace and texture, to keep the Coarse Grid and Fine Grid at small enough values to avoid funky artifacts. You'll also need to set the Ocean Detail to at the very least Video Detail. Don't expect a fast render.
I'd suggest that you set up your project with the logo as an image map set to Displace using the Alpha of your logo with the intensity set to 0. Then when you've got it raised out of the water enough, split the layer (Ctrl/Cmnd + D) and change the image map to Displace and Texture Below. Overlap the two copies by adjusting the out and in points so the wave action matches. This would fade in the logo color in like it's coming from below the water. As the logo rises farther out of the water split and overlap the layers and pick Texture Above or Texture On to achieve the look you want.
The Logo is going to bend just like the water, but the color will be there. If you need to morph the logo to a flat surface then you'll have to match the angle with another copy of the logo as a 3D layer then carefully transition between the two. With Psunami you'll never be able to make it look like the water is running off the logo. You can fake it fairly well.
If you need to have the water run off the surface my suggestion would be to do this in a 3D app. Blender (free open source) has some pretty good water effects and there are a bunch of tutorials. Depending on the realism you're trying to achieve you might want to composite some actual footage, some 3D, and some Psunami. This is definitely not a one click, one setting, one layer, two keyframe project.
Just for fun I set up a project using CS5. It took about 5 minutes because I did a lot of this kind of stuff a long time ago. You'll find the file HERE. I hope it helps. The resulting image looks like this:As you can see the logo moving along with the water and it still looks submerged. It takes a bunch more work to make it look like it has move up and out of the water.