You can have your whole pay, or partial pay paid into a German bank. You are then paid this amount in Euro. The exchange rate is dependant on the FFR (Fixed Forces rate). This decides the exchange rate to which you are paid. You can elect to have all your pay into your UK account and transfer the money yourself, but you will loose as you will then be charged a fee each time. Best way is to stick with the FFR, have an allotment sent to your German bank (enough to live on) with the remainder going to your UK account to cover direct debits etc..
Of course, it is all dependant on your circumstances