I am recording live kit with hats, top and bottom snare, toms, overhead and room mic.  What is the more professional sound, taking time to clean up all the bleed from other tracks and have just the hits or leave the bleed and gate the mics best you can?  I am learning towards cleaning up the bleed because I am playing drums in a bedroom so I don't have much space for the sound to travel so I have a lot of bleed.

The mix techniques are endless. The most common\basic starting point would be to

• Gate the spot mics. Make each hit open and resonate naturally.
• Balance out the spots mic levels of overall the kit.
• Bring up the overheads\room mics to fill everything together. 

EQ & compression is equally part of the modern drum sound.
 
Tips

• Compress the hell out of the room mics "smash" them with an 1176.
• While mixing It's not all about the spot mics.
• Hat mic is unneeded 95% of The time. Overheads\rooms cover it.
• HP overheads
• Learn to hear phase issues.
• LEARN TO HEAR PHASE ISSUES.

Eric covered most of what I probably would have said... Also sort of depends on the style of music you're recording... Really fast precision prog-rock / metal would probably require more gating / cleaning, than say... a Tom Petty record or something... But half the fun of recording drums (if you actually consider that to be FUN), IS the experimentation really.  Just mess around with stuff, and see what works, but like Eric said, the more mics you have, MAKE SURE YOU DON'T IGNORE PHASE ISSUES. 
 
But I'm curious, just because I'm a drum recording / microphone geek, what exactly are the mics you're using for everything?  I don't generally get a chance to talk microphones with people on "digital recording" forums these days, so my ears always perk up when I hear someone say they're actually miking things these days.  (I mic EVERYTHING I possibly can...)  SO YEAH!!!  MICROPHONES!  WOOOOOOO!!!  *high five*  Sometimes I even mic the studio monitors, just to experiment with random tones & colors. 
 
Microphones...
 
*sigh*
 
So dreamy...

BLEED MAKES IT REAL! One of the things that most people didn't realize with older drum machines was the individual drum samples had no bleed in them. Picture a guy in a studio with just one drum at the time hitting that tom until they got the perfect hit. No velocity layers. That's what makes them sound so fake to my ears. I was so glad when I stumbled upon a drum sample library that I built in to a Battery kit. When you hit the any of the toms you could hear the snare rattle. When you kicked the bass drum you could here the toms ring sympathetically. When you hit the snare, etc. Take all that clutter in there and it sounded light years ahead of any drum machine out there. I actually had people ask me where I tracked those drums at. Now we have bleed controls in just about all software drum packages. Bleed is our friend.

I agree with that to a certain extent (like I said, for Tom Petty style music, as an example)... "Natural sounding music"... But sometimes, with crazy fast prog rock drummers and stuff, that bleed can get muddy REAL quick, and you won't be able to hear the tom hits, if you have 8 tom mics, 2 snare mics, hi-hat, ride, 3 kick mics, 7 room mics, etc... (just randomly throwing numbers out at this point)...
 
But to a certain extent, (for THAT kind of music), that's sort of what the room mics & overheads are for... You'll still hear that "bleed" through the room mics and stuff... But if you're individually miking every piece of the kit (sometimes including 2 mics on each tom, top & bottom, etc...)  Then bleed can quickly become that friend at the party that you'd rather not have to deal with, because they drink too heavily or something...
 
But yeah, other times, it's nice to just have a kick mic, snare mic, and a room-mic, and go all natural or whatever... It REALLY depends on the style of music you're mixing. 

I usually edit out bleed from tom mics. Makes it easier to do radical EQ and compression on them without adversly affecting the overall sound of the kit. Use a close room/FOK mic to restore lost "naturalness"

Having only one project at a time is I think the way to do it.  However I think there is some strange happening with the Step Seq....See this post.
 
http://forum.cakewalk.com/Question-about-Drum-MapStep-Sequencer-Annomilies-m2901667.aspx
 
cheers

+1 to what Eric said. (Especially about phase issues.)  
 
Bleed can be your friend and if you're doing a true live recording, you have to do your best to work with it. 

I hate bleed and I mic hi-hats, but that's just me.  I like isolation but it depends on the style you are going for.

konradh! Nice icon there. I've had mine on for a while and been thinking about changing it!