Can't control track volume/pan from Sonar X3 during recording

"We are forced to use the volume knob on the Focusrite Scarlett 2i2 to adjust input volume during recording."
 
This is the correct way to control input level during recording.

Do you have Input Echo enabled on the track(s) you're recording?

No, because the latency it introduces is distracting.

The 2i2 is very limiting for recording more than 1 person. I believe it does not even use mix control software which is where your monitoring is controlled with the upper models like my 6i6. 
 
You could record a stereo drum track and all you nee to do is monitor the output and listen to Sonars metronome or a drum track in the headphones. This is what direct monitoring is for, do not use input echo.. 

Of course I have used the metronome. But, I prefer to start a song using a simple drum pattern instead. I have dozens of patterns I use instead of the metronome. I see your doing something similar using the kick..Why not add a hi hat or even a snare too?  Much easier to play tight to a solid loud percussion track.
Is it your having trouble with the volume of the headphones??
If so think about using a small mixer or headphone amp to kick the level up a bit.
 
 
A comment on your "panning the 2 instruments???
You should always record mono for mono sources. Do not use stereo unless its a stereo source like a piano, synth or guitar effects pedal.
A bass is a mono source.
Insert a audio track and select
Focusrite Mike 1 left for the bass
Focusrite Mike 1- right  for the Cajon. 
The 3rd choice is Focusrite mike 1 stereo do not use that for bass or 1 mike.
My self I would record the Bass first in mono and then use 2 mikes on the Cajon
They sound like a whole kit if you hang a condenser above and put a kick mike on the back.
 
Even though you only have 2 channels you can do a huge recording one part at a time.