Stereo Master Buss & Clipping Issue

Hi;
 
I use Sonar X1 Studio.  I recently did a 24 track audio project.  Actually it was an existing project from another DAW that I converted to WAVs and did a remix in Sonar.  I took notice that there was no stereo master.  It bounced the tracks fine, but I still would like to have a stereo master track in the project.  My question is how can I create one (without redoing everything I've already done) and how would I route the individual channels to the master?
 
Also, in this project I took notice that after I rendered the project to a WAV I heard several clicking sounds scattered throughout the song that I didn't hear in the open project.  Upon opening the WAV in Audacity, I saw that these clicks were where there was clipping.  I went into the project and reduced the volume on the instruments where the click was and that seemed to correct the issue, but I had to reduce the volume of the track at the clipping point lower than I wanted it to be.  I found it strange that the clipping occurred in areas where the volume of that instrument wasn't overly saturated to begin with.  I tried compression but that just made it worse.  Any suggestions to remedy this, hopefully with a utility that is already in Sonar x3 Studio's toolbox?
 
Thanks
 
John B.

Question 1 - You can click on the output (O) of any track and "Route to a New Buss," name that buss "Master" and have it output to your audio interface (what the track is now). "Master" will then show up in the output dropdown of each track (I do not think you can do them all at once with X1 unfortunately, but cannot remember for sure).
 
Question 2 - There are a few methods to use. Compression by track (just to catch the peaks), and limiter on the Master buss (for the same reason). I forget offhand which ones were in X1 though. If this is an export only concern, Limiter No6 is a good free limiter you can put on the master buss to prevent clipping (and has several presets you can try).

So this is what I think you are doing.  You opened  the midi file that was created on another DAW into Sonar as midi tracks, and then insert soft synths to play the tracks?? correct? 
But somehow you are saying you "converted" the midi to audio?? this part is not clear. 
Did you bounce each track to audio? This is not nessassary in Sonar as you can just export the midi song and it will create a Stereo wave file of the song exactly as it sounded when played. 
 
If the original song used GM midi then TTS-1, as example, will play the song more or less the way it was composed. You simply OPEN the file in Sonar, insert TTS-1 and set all track outputs to play it.  If there is peaking then you need to turn some tracks down. 
Bouncing was used more in the past when we wished to reduce CPU load. Not really needed anymore unless your going crazy with 25 soft synths. 
 

First the clipping issue: 
So it sounds like you just solved this yourself!  
Obviously your rendering of the tracks with Melodyne resulted in overs.  
 
"but I still would like to have a stereo master track in the project.  My question is how can I create one (without redoing everything I've already done) and how would I route the individual channels to the master?" 
 
 I think your asking 
"How do I insert a Master Buss and how do I send all the tracks there? " 
 
Well inserting a master buss is easy. Left click the buss pane ( found below the track pane)  and choose create a new stereo buss. Then name it master  or My Dog Spot or whatever. 
And it's pretty straight forward to assign any track to any buss. Every track has an output. If you had no master buss then the default will be your audio interface 1/2. So change all the track outputs to the new Master (or my dog spot) buss.  If you highlight the whole project ( ctrl A) you can do this globally using the "tracks" -audio output drop down. . Hope this was what you needed. Cheers.