2 mics into a BR800 with USB to Sonar?

I tried to record with 2 different mics for the tonal variation. 
A condenser(Apex 460) and a shure sm 58.
I'm using my Boss BR800 as the controller.(4 inputs)
I used input 3 & 4 because 4 has the Phantom power for my Apex
I set the input mode to "4 track record" because the "1 & 2 stereo" choice does not include #4
I set up 2 Audio tracks in Sonar, one left one right.
I do get both to track in Sonar but they sound suspiciously similar in tone and the waves look identical.
Also when I subsequently pan the two left and right there is no separation making me think they are identical. Maybe even a blend? IOW the two mics into each track?
Maybe there is not much difference in the mics but I'd be very surprised.
How does Sonar know to use those two channels separately and which is which?

Thanks Jesse,
I appreciate the answer.
I've been reading the hardcopy manual that came with it all morning and I don't see where it specifically says that signals will go, for example, from input 1 to track 1 on the DAW and input 2 will go to track 2 on the DAW. etc thru to 4. For example I see on pg 37 it says "4track rec" that 4 tracks will be recorded simultaneously and you do get 4 tracks onto the BR800 if you use it as a stand alone recorder but does not say if it will be blended into 1 or 2 tracks if sent thru the USB to the DAW.
What would be assumed?
Further ,and maybe related,
In Sonar, in the In/Out area, is the left and right BR800 the only DAW control I have on this?
IOW if I was to do 4 tracks, How would I get 4 simult.from the BR into Sonar if it only has left and right.
I would expect The Sonar Input to list all the inputs on the BR so i could match them up.

I'm probably over thinking this but don't know what to assume in the signal path between the two.
I may also be confused the BR 800 option to use it as an Audio interface or as a controller. Both modes seem to be able to record to Sonar.

Thanks Jesse
I have been using the BR800 for all audio for a while now. It's great.
A much nicer sound for my KRK Rokit 6's.
I do know how to select the various inputs too. 
I've been using it as a stand alone, as an input device to Sonar and as a controller.
The issue is using 2 mics at once but one of them having to use input 4.
The choices are only 1 & 2 for stereo or 1 thru 4 for 4 track recording.
I've also tried 1 & 2 which works but I get the same lack of separation.
I need to test them by separating them further to see if they are working but are simply too similar to tell a diff.

IF you are recording vocals, 

Input 1 R
Input 1 L  = use any chanel
---------------------
Input 2 R
Input 2 L  = use any channel
---------------
Input 3 R
Input 3 L  = use any channel

Input 4 R
Input 4 L   =  Condensor mic ( use any channel

Make sure under Sonar preferences (Audio) that you select the inputs you want available first. Now these inputs should be available under each track to select in Sonar. 

Peace

M_Glenn_M


Aha! That sounds promising. One more thing? I went to preferences and looked thru the whole list but could not find where I could chose available inputs.

Inputs are found in Windows Control Panel - Audio- Sound.  Click the appropriate tabs for recording and playback at the top and then select the BR-800 for inputs and outputs.
 
Peace

hello
 
mr  M_Gelln_M
 
Did you find the solution ?
 
I have same your problem exactly
 and I tried every thing ,
 
I want you please