Well I figued out part of it. To flaten the ocean floors you need the bumpmap and the specmap. Be sure you leave the specmap so that the seas are in black and not inverted so they are white. This should be the default image you get from LunarCell. Now take a look at the bumpmap and look for the color that best guesses sea level. Its going to be gray it just matters what shade of gray. I used photoshop 7 for my work but I guess it could be similar in Gimp. Open both the bumpmap and the specmap in photshop. Adjust the contrast of the specmap so that the black areas representing the sea turn to a shade of gray that is close to sea level on the bumpmap. Now use the magic eraser and select the white section of the specmap and click. This should make it go transparent. Select all of the image and past it over the bumpmap. Be sure your specmap and bumpmap are both the same kind of file. Such as .jpg or png. I use .png for all my work. Make sure the new layer is fully covering all the black in the bumpmaps sea areas. If it doesn't and you see some black on the bottom or the top undo the paste and go back to the modified specmap and try seleting a little less. What I am saying is as you start to select shave a little off the top. From each time I tried this it always seemed to place the layer to low. Now try again. It may take a few trys but when you have all the black in the seas coved you will see when it looks right. Now flaten the image and you can start to either use the blur tool of if you have photoshop 7 use the healing tool and start blending away the faint pale gray lines that were left behind after the layer was pasted. When you get all finished save it as a .jpg. Plug it in as your bumpmap in whatever .ssc file you are using and take a good look. You should have smooth waters. I know it sounds like a lot of work but trust me the end results are much better than the orginal bumpmap the LunarCell gave you. Also tweaking the contrast and brightness of a bumpmap can give it added depth but do it only in moderation or your mountain tops become flat topped measas instead and you could undo that nice flat sea floor you just made and create a whole new mess.
Heres is a sample of what I did. First is the stock LunarCell bumpmap with bumpy water.
Now my modified bumpmap. Smooth waters.
As you can see there is a great diference. I don't know what the white dots are in the second image. Just some kind of noise that got included with the screencapture. If you read this and can think of an easier way please be my guest and maybe fill everyone in on the info.
Oh and as far as using only the bumpmaps for terrian texture. I have found after several diferent atempts that in LunarCell if you at least give just a little hint of a shadow being cast on the texture and using the bumpmap generated you get a much better result. The more shadow you generate the greater the detail and the less important LunarCells poor bumpmaps become to a point. The bumpmaps are a must for proper lighting effects at the planets terminator. That is the transition from light to dark on a planets surface. Besides from what I have seen of all the Earth textures they all have some shadows apearing in the mountains. There are even shadows on the Moon textures as well. Hope this helps out and answers any questions.