Should #1 go to the front brakes and #2 to the back? Or does it really even matter??

 

Yes it matters

Rear of master's line goes to front brakes, front master line goes to rear brakes

Has to do with fluid loss, rear chamber in master is more likely to retain fluid longer if there is a major leak
And there are 2 lines/chambers in case front or rear has a leak, so you won't lose all braking, still have to pump the pedal but brakes without the leak will still work