It's normal in SONAR.
So, can you select input 1 independently of input 2 in a track?
If so, you can use input 1 of 1/2 on the first track, input 2 of 1/2 on the second track and so on.
You can also rename the tracks if you want. Change Track 1 to Track 1/2 if it will help youi keep track (

) of things better.
As for the output only sounding on the left, are both of the output meters (L/R) showing signal but you can't hear the right, or is just the left-side meter showing signal?
If the former, check your cables/connections. If the latter, make sure none of the tracks are panned all the way left.
If you recorded mono instruments on those tracks (mic, guitar) in a stereo track, you will only hear the left. Record those instruments on a mono track, either input odd or input even.
If you don't want to re-record those parts, Bounce the tracks to different tracks using the Split Mono preset. That will render the L/R signals to 2 different tracks, one being the sound and the other being the channel with no sound. Then delete the 'no-sound' track.