Li-Ion batteries are not sensitive to how they are cycled and do not require any kind of charging regiment. You can charge them anytime at any voltage level. So yea, just throw them back in the charger when they get too low for the booster.
I think you're confusing Li-Ion batteries with with NiMH or NiCad batts which need to be fully cycled to avoid "charge memory". For Li-Ions, they actually wear less when not discharged deeply.
I'm a heavy vaper and use about 250mAh per hour so a 900mAh 14500 would last me a little under 4 hours. So, it depends on how you vape. For me, 5 hours would be excellent. For a light vaper, 5 hours might be low.