As for cleaning, your best bet is to remove the stem and bowl, and put that in boiling water. For the actual bong itself I'd say just scrub it real good with some sort of course material and some rubbing alcohol. If you use alcohol make sure you can smell NO trace of alcohol in the bong before smoking out of it, or you could take your lips off.

With bongs I usually change the water after every smoke. If it's a particularly large session then I will change the water half way through. I hate using dirty water.

I wouldn't be so worried about the bong water making a smell, but more-so the actual bong itself. If you use it and never clean it (though as you said, you are a bit of a clean-freak so that shouldn't be a problem) then there will be a smell issue. So long as you clean it after every 4 or 5 sessions (and change the water after every session, and not leaving water in it when it's not in use) you should be fine.

Congrats on the new bong btw - got a name for it yet?