Best practices when hosting visiting speaker (especially with the questions part of their talk)
First of all, stop worrying - I am sure that, no matter how you decide to approach this, the quality of the talk will be much more memorable to the participants than how you ran the Q&amp;A part from an administrative point of view.

Further:


  I thank people for coming and introduce the speaker.
  I sit down and the speaker... speaks.
  At the end of his talk I stand up and ask if there are any questions. If people > raise their hands I'll point at them so they can ask the speaker their question. > I'll keep an eye on the time so when there are just a few minutes left I'll say "there's time for just a couple more questions".
  After the last question, I'll thank the speaker again and that'll be it.


This is pretty much the standard layout of such sessions, and I see no problem at all with running it like that.


  Should I be doing the questions? Or should I let him call on people himself?


It is more common that you as a "moderator" call the questions, but I have certainly seen it handled differently as well.


  Should I just stand to the side of him? 


Probably not during his talk, but when you are moderating the Q&amp;A part you may get up the stage. However, most moderators seem to prefer to stand somewhere to the side, presumably to not steal the presenter's thunder. 


  is it ok for me to ask questions (particularly if nobody in the audience is doing so)?


Yes, you should make sure that you have at least a few fallback questions as a discussion starter.