If I reverse mount a Canon 50mm F1.4 prime lens on Canon Rebel T3i/600d can I still use manual focus for macro?
We have a great blog post here at our own photography stack exchange blog that explains the process very thoroughly: Take macro shots like this for less than the cost of a pizza
To answer your question, yes you can still manual focus, that is the only option as autofocus will not work when reverse mounted. Manual focus is a bit odd feeling, because the mount is so small and doesn't really give a solid "mount" feeling as a normal mount would.
You don't directly have control over aperture, but you do on a Canon body by using the depth of field preview button(Using tack on a Nikon lens). The blog post listed above has the details on how to achieve this specifically, but it is a very nice "hack" indeed.