I have found a solution... It was a two step process. First I set the spatial analyst extents to be the same as the larger DEM raster. Then, I created a conditional statement in the raster calculator to only save the cells from the second raster that were greater than the first. Then I used the mosaic to new raster tool to replace the cells in the DEM raster with the levee top raster cells that were higher than the existing DEM.