Most ebike batteries will have their own low voltage protection built in to the battery's
BMS, so you can set the controller's low voltage protection setting as low as it will go
(32V for a 48V battery pack) and the battery's
BMS will cut the power to the controller if the battery's voltage falls too low to prevent damage to the battery.
But, if you are using a 14s LiPo pack
without any form of
BMS protection, I recommend that leave it set at 42V
(3V per cell).
Lithium cells do not suffer from "memory effect" like NiCd
(and some NiMH) do, therefore it is not necessary to fully discharge them.
In fact, fully discharging a lithium battery every time
(and/or keeping it fully charged for long periods of time) has been proven to reduce the total number of charge/discharge cycles available from the battery.
It is much better for the battery if you can leave at least 20% of its capacity unused and only charge it fully if it is going to be used the same day.
Charging it prior to setting off each morning would be better for the battery, as it would help to keep the cells nicely balanced
(as well as ensuring you don't run out of battery on the way home if the battery capacity is only just enough to complete two return trips).
Ideally, your battery capacity should be at least 20~40% more than you will typically use on your regular trips to achieve a longer lifespan from your battery
(and it keeps a little in reserve in case you need it to cope with a strong headwind).
If your regular return trips require 7Ah, then your rated battery capacity should ideally be at least 10Ah if you want your battery to last a long time. Completely draining a smaller 7Ah battery will reduce the number of cycles before your battery needs to be replaced
Basically, if your return trip only draws 5Ah from the battery, then it is much better to use 50% of your battery and then recharge before the next trip, instead of trying to complete two return trips on a single full charge.
However, if your return trip only draws 3~4Ah from the battery, then it is probably not as bad to use the battery for two return trips before recharging.
Check out
Micah's video for further information on extending your battery's life.
Alan 
