@Stealph: You can use Mission Control, Diagnostics, Battery to see how many charge cycles have been registered in your original battery. Try to ride more often on the new battery than on the original one, and rotate them sometimes or when necessary to increase the range. At some time both batteries will reach a similar number of charging cycles. Such practice will help making both batteries live long.
Now: It would be
ideal to keep each battery charge between 20 and 80% but if you ride for big distances or using Turbo support mainly, just recharge both batteries as you wish. Batteries are there to be used
(If you don't plan winter riding, keep the batteries in some storage at room temperature, the best at 60% charge, and give both of them a short charge once in a month.)
Good to know you can ride without the battery cover. Mind sharing a picture?