Would the solution be to open 2 instances of AD?? One for the Base and one for the Snare?? For each of them 3 Tracks, Base, OH, Room, let us forget the Bus! Then group them together, 3 for Base, 3 for Snare.
 
Hmmmmm, now that I write it down, it could be the solution:)
 
Maybe, I'll give it a try tomorrow!!
 
Bassman.
 

Slugbaby has summed it pretty well. The overheads are a set of mics, instead of say and fx send. If you work in the mixer I AD2, you still have the same situation. It's only when you go into the instrument editor itself, that you control the amount of bleed from the bass, or the snare. The bleed in the overheads from the Bass, Snare, hats and Toms, are for tone. So when you have the over all sound you want, for say the bass with the bass mic, the bleed into the overheads and the room mics, then you don't generally want to change those levels separately from each other.
 
If they all feed into a drum bus, you can then automate this. and keep the tone of the kit, but change the volume in the mix.
You could also automate the Volume of AD2 in the midi track, and that would effect the whole kit. That would change the toe subtly if you are using compressor on the faders
If you want individual drums to be played softer or harder dynamically, then Velocity would be the way to go. the tone would change, but it would keep the balance between the individual drums and the overheads and room. And would sound more natural.
 
You don't mention hats or tom, even though they spill into the overheads, I wouldn't treat the overheads as a hats and toms source. The overheads pick up the cymbals, and spill from the kit.
 
I set mine up as
All mono
1 Bassdrum
2 Snare
3 HiHat
4,5,6,7 Toms and group the faders (I set their pans, then hide 5,6 and 7 to keep it tidy)
8 Flexi 1 (hidden)
9 Flexi 2 (hidden)
 
All Stereo
10 Overheads
11 Room (I don't always use this, as I feel it's basically a reverb, and I am using 2-3 reverbs to ty the whole mix together, so I don't room from the drums is another reverb that no other instruments can share. Also I mix and match the drum kits in AD2, and they weren't all recorded in the same space)
 
I don't use bus as I'm using the console in sonar and it's fx, the FX in AD2 are turned off 
 

I don't think the OP is looking for the most realistic sounding/working solution. He's going for a specific effect and it's kinda tricky to do.

EDIT:
Here's a thought - if you don't like that using midi velocity changes the timbre, you can modify that in AD2, making it so that all different velocities trigger nearly the same sample. This will still allow you to use midi velocity to control volume.

Sanderxpander
I don't think the OP is looking for the most realistic sounding/working solution. He's going for a specific effect and it's kinda tricky to do.

If he's looking to change the OH and Room feeds mid-performance, I don't know if that's possible in AD.

After trying, thinking, thinking trying I come to a result:
 
1. two instances of AD, one for the Base one for the Snare, grouping Base Track, OH level and room Level together!
 that works for Base and Snare, not if you do both together in one instance!
 
2. Make Envelopes of Base Track and the automation of OH and Room Level and increase or decrease them together
 
I don't see any other solution!!  But thanks for all who was involved in thinking about:)
 
Thanks,
Bassman.