Some questions about stereo tracks used for reamping.
 
What I would like to do is create stereo tracks, the left side is the DI, the right side is the miked signal.  I like to work this way because it keeps clips organized.
 
1) When recording a stereo track, is there a way to assign the left and right with non-contiguous inputs?  The DI and mic pre are not a stereo pair.
 
2) In SONAR, how would I take the R signal and center it?  (Also need to mute the left)  Basically I need to have independent pan control of the right channel asif it was a mono track.
 
3) Is there a facility to link clips together so that when one is copied/moved, so is the other?
 
 

1) Need more info - what kind of interface, what kind of outputs from the gear. For example, with the TASCAM US-2x2 or Roland Octa-Capture, the inputs are mono but paired. So for example, you would plug your DI into input 1, your mic pre into input 2, then select inputs 1+2 in SONAR to have one on the left and one on the right.
 
2) The Channel Tools plug-in will do what you want and more.
 
3) Sounds like Selection Groups is what you want. This seems to be a SONAR feature a lot of people overlook.

"What I would like to do is create stereo tracks, the left side is the DI, the right side is the miked signal.  I like to work this way because it keeps clips organized."
 
With most DAWs you can set up your I/O, or Ins and Outs with just about any routing matrix that you can dream up, and you can even name the In and Outs with the exact names you wish to see when you are selecting inputs on your tracks. For example; you can use analog input 1 and analog input 5 and assign them as a pair which you name "Guitar", and you can record input 1 and input 5 as a "stereo" (I'd prefer to call it a dual mono) track. As you say, this can be a convenient way to keep the tracks organized.
 
Sadly, you can't do this with SONAR.
 
You can't even name the ins and outs in SONAR and see the exact name you have assigned. You can name the inputs and the outputs but what you'll see is your name with extra labeling attached. Stuff like "Left" or "Right".
 
It's a bummer, and It's been like this for close to twenty years. Some folks are so used to it, they don't notice the inconvenience. I am am reminded of how much friendlier the other DAWs are each time I use one.
 
There's something really cool about about plugging a mic in to the XLR connector labeled analog "input 2" on your hardware and then assigning analog "input 2" in your DAW's track. Simple. Sensible. Easy to remember. 
 
 
 
 
The work around for you will be to record two tracks as MONO and then convert or bounce them to "stereo" two tracks. You'll probably grow tried of that, so maybe you can consider using a folder as an organizational aid. It will waste a lot more screen real estate... but that's another story.
 
   

200bpm
...What I would like to do is create stereo tracks, the left side is the DI, the right side is the miked signal...
...how would I take the R signal and center it?  (Also need to mute the left)  Basically I need to have independent pan control of the right channel asif it was a mono track...

If you have a stereo track with DI left and mic right, you can set the track to mono (by clicking the Interleave button, which is visible in Console View or in the Track Inspector). Use clip automation (i.e. clip pan) to control the balance between DI'd and mic'd signals.

On the other hand, if you want to use the two signals separately, you can Bounce To Tracks and select the option Split Mono.

mike_mccue
Some folks are so used to it, they don't notice the inconvenience.

Another possibility is that the need to do this is sufficiently rare that few people care. It's up to the OP to decide if "You would plug your DI into input 1, your mic pre into input 2, then select inputs 1+2 in SONAR to have one on the left and one on the right" is that much of an inconvenience. As far as I can tell he's talking about 2 mono sources.
 
For me it doesn't matter because regardless of what DAW I use, I have enough audio interface inputs that everything's patched in and I don't need a patch bay. That setup also makes SONAR's Selected Track Inputs feature a useful time-saver.

The part many people no longer notice is that in SONAR an XLR input labeled "analog input 2" on your hardware will show up as something like "Right analog input 1" in your SONAR input selection dialogs.
 
After the first 15 years, you kinda get used to it. ;-)
 
 
 
 
 
Regardless of how few people may care to do something, doing exactly what the OP has asked about, "When recording a stereo track, is there a way to assign the left and right with non-contiguous inputs?", is easy and breezy in the other 3 DAWs I use and it's easy in a few DAWs I don't use. You just set up the I/O to suit the way you wish to work.
 
 

I think the track assignment system is a ASIO driver issue, not Sonar. I get the exact same list in Cubase. 
It certainly has never bothered me, I don't even think about it. If I plug into input #2 I will assign  Right #1 as the track input. 
 

Arguably this routing matrix is a function of the hardware interface rather than the DAW. The reason it isn't in SONAR is because many professional audio interfaces provide such a matrix that allows you to group channels into logical DAW inputs or outputs. RME, MOTU and Lynx are some that come to mind.
I havent really seen a lot of requests for this matrix functionality in SONAR probably for the same reasons.. Also I can see the use case but it isn't such a common requirement to want to record non contiguous channels into a single stereo wave. The question to the OP would be why not use contiguous channels on your audio interface - is there something preventing you from doing so?

What is wrong with having the tracks as mono next to one another? Name each what you want. They are mono anyway.
 
I don't see a reason to use stereo.  

As I've mentioned before, I use Ableton Live for live performance and consider it a very innovative program. However, it's the worst program for hardware assignments because there is no way to change the labeling. If you have an input with a ton of I/O, often the master L/R will be considered output 1+2. So what's labeled output 1 is what Live considers 3. Every time I test a new interface with Live, I have to plug things into different inputs and outputs, and enable inputs and outputs in Live one at a time so I can draw up a chart of what relates to what.
 
As to a matrix input, I agree with Noel...most interfaces have applets to do the routing, and handle situations unique to particular interfaces. Personally, I find setting up a matrix within a DAW annoying. It's simpler for me just to assign a track to an input.