Historian Ruth Goodman addresses this in her book "How to be a Tudor." Handily, that chapter is actually excerpted online! It seems kind of silly to repeat what's said there given the length of the article, so check it out.

Short version: scrub-downs were preferred over full body immersion baths, and if your clothes aren't full of sweat, you won't reek of BO (at least, not enough to be noticed over the smell of everything else).