Well assuming we don't talk you out of using a canister (not in vogue with reef tanks - and not really necessary if you have a sump, skimmer, etc.) ...
1. what should i have in my canister filter and what shouldnt i have in my canister filter in terms of media?
In terms of what not to have, I would not go with anything that is not really porous and would clog. I would not overpack.
I used to use Eheim media on the bottom - forgot what it is called but it looks like little cylinders. Surface area stuff for bacteria. I suppose if you don't use that you could use bio-balls or the like.
Then I used a holding tray of carbon like media.
Then topped it off with floss. Quite a bit of floss.
2. when i clean my canister filter out should i get rid of the water in there or is it good for the system to have that "crap" in there?
3. when i clean my canister out should i be not rinsing anything out?
I tended to leave about 75% of the water on a general cleaning that I would do once a month. During a monthly cleaning I would replace the floss only most of the time - sometimes I would replace some of the carbon depending on my bio-load at the time.
Every other time I would replace most of the carbon too.
Once a year I would pull everything out keeping the Eheim media in a bowl with some of the water... clean out the canister. Lightly stir and toss some of the water from the bowl with the Eheim media, then put the media back in. I would NOT replace the carbon until the next monthly cleaning. Replace floss and repack.
Be sure to wet the rubber ring gasket prior to sealing. I would do this with a little freshwater on my finger going around it.
Basically you don't want to over sterilize when you clean it. There are, as you mentioned, beneficial bacteria and 'bugs' in there that you need to break waste down and break ammonia down, etc.
Hope this helps.
canister filters 
