Hi,
 
I have two pads in a single Omnisphere instance and I want to route a MIDI channel to each and have the audio of each part route back to its own audio channel.
 
I have no issue achieving this with Native instruments Battery but I just cannot get it to work with Omnisphere.
 
Please help

EDIT : I want different MIDI sent to each "PART" but only CHANNEL 1 seems to get MIDI.  If I set a part to channel 2, nothing is received

This probably isn't what you're asking, but just in case, A and B layers cannot be driven with separate MIDI channels nor routed to separate audio outputs; they are considered a single voice. 
 
More likely, you're asking about Multis. There, you have 8 slots, each of which can hold a separate patch that can be routed to any of Omnisphere's 8 audio outputs. By default, each is assigned a sequential MIDI channel (slot 1 = MIDI ch. 1, slot 2 = MIDI ch. 2). By default, they all go to OUT A, so you'll need to specify OUT B for the second pad.
 
You cannot do this with an Instrument Track. You must use 4 separate tracks, 2 MIDI and 2 audio. 

I do this all the time with Omnisphere and its no trouble at all. Verify your process for us. How are you loading the instrument initially? Are you using a simple instrument track or separate midi/audio? When you create the midi track for the channel 2 part, are you setting its output to omnisphere?

From the limited information you have provided it sounds like you are using the default simple instrument track. Omnisphere does not like this and you have to have separate midi tracks and potentially audio tracks if you don't want everything coming out of audio channel A.
 
Therefore don't insert Omnisphere as a simple instrument then add a separate midi track, change that midi track's channel to 2 and the output to Omnisphere. If you still have problems I could try and do a video or send you a cakewalk template with Omnisphere already set up with 8 part multi.

Yes, I'm using Multi's and yes I use two different midi channels and 2 audio channels but as soon as I set part B to ch2, it does not receive any MIDI even though both MIDI channels are set to Omnisphere.  The outputs work correct so part A and B goes to separate audio channels but I cannot receive ch2 MIDI.

The reason I started going down to less instances of Omnisphere is because the more I add, the more "MIDI dropouts" i get throughout the projects.  For instance, at playback, my Kick plugin would skip beats or my Omnisphere SUB would just not play certain notes.  With each playback, its different notes.  My CPU usage is almost negligible, and the "audio" doesn't drop, you still hear previous note's reverb for instance, but like the MIDI notes just disappear..
 
Should I keep the instances of Omnisphere to a minimum?

RedSkyRoad
Should I keep the instances of Omnisphere to a minimum?

Depends. One of the current limitations we live with is that individual plugins are only able to use the processing power of a single processor core. So if you have a speedy quad core system, a single instance of Omnisphere will only use one of those cores. In cases like that, you will probably see better performance if you spread your 4 Omnisphere parts across two instances as opposed to loading all four parts into one instance.

On the other hand, if you're running a slow dual core althon chip from days of pet rocks and beanie babies, you'll probably do better to keep the plugin count to a minimum.

RedSkyRoad
The reason I started going down to less instances of Omnisphere is because the more I add, the more "MIDI dropouts" i get throughout the projects.  For instance, at playback, my Kick plugin would skip beats or my Omnisphere SUB would just not play certain notes.  With each playback, its different notes.  My CPU usage is almost negligible, and the "audio" doesn't drop, you still hear previous note's reverb for instance, but like the MIDI notes just disappear..
 
Should I keep the instances of Omnisphere to a minimum?

This sounds more like an incorrectly set MIDI Prepare Buffer in SONAR - try increasing of descreasing it (I always forget which direction solves this!).

JohanSebatianGremlinOne of the current limitations we live with is that individual plugins are only able to use the processing power of a single processor core.

kontakt and (i think) some u-he plugins are multi-core aware/capable