You could set the hot end fan to run off w/ the control board fan. Then use the part cooling fan w/ the existing fan wiring. You'll need to set 'M106 S1' in your starting GCODE so the part cooling fan doesn't run all the time. If you are printing PLA or whatever, just have it turn on layer 2 as you normally would.
Having the bowden tube seperate just makes it easier to clear a jam if that happens. No real other benefit as far as i know.