How to maximise the life of the Apple battery charger set (for Magic Mouse) batteries?
Lithium batteries do not like complete discharge, so do it at 10% or higher. You can leave them as long you wish in the charger, it will stop charging when full. 

The battery charger it self has no limit on life time, yet again, it has to work harder if completely drained battery is to be charged.

If for some reason you have to leave the batteries on the shelf (in the box) for longer periods (months) then do it a 40% charge and keep them cool (15 Dgr. Celsius preferred).

Then when you notice the ones currently in use are at 20% start charging the replacement (from the box).