Sarah -
I think both themes can be used. One for your ceremony and one for your reception liike you said. This way you get the best of both themes! Think colors when trying to do themeing. For your ceremony find B&B clip art adn stick with golds and reds for colors. You can add little things like candle sticks and cute little items on programs or flower petals cones. your flowers can be reds and golds.
Then for the reception at the LS - love the venue! - do your under the sea theme. They ahve a beasutiful cake themed to Under the Sea and you can alter it to add nemo in. In terms of decorations there you need very little just centerpieces. Each table could be named a different under water Disney character - nemo, ariel, sabastien, etc. and have a cute piece of clip art on your table cards. then the centerpieces could be simple or themes as well. There are a lot of under water items on line. I was going with an underwater theme for awhile. But now It is just the blue coloring of the LS that has stuck. Good Luck and have fun. HTH