Water up to the line between his top and bottom. They float, but you don't want it too deep just in case and you don't want it too shallow either because you limit the benefits. I like to put my guys in the bath tub or a container on a slant to provide different water levels. My leos LOVE to swim in the deep end while the Sulcatas will sit on the shallow end and just chill. From my experience with Leos from 2 different breeders, Leos LOVE swimming!
Soaking needs to be done in a separate opaque tall sided tub. It needs to be done somewhere warm so the water doesn't get cold during the soak.
Putting your tortoise in its water dish is not soaking.
Your water dish is too deep with too tall sides. Some tortoise will die of dehydration slowly over time rather than drink from a water bowl that they don't feel comfortable with. The immediate threat of drowning overcomes the long term threat of dehydration. I like to use terra cotta plant saucers sunk into the substrate. They are about half as deep as what you are using now.