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.