deployment softwares

I've been deploying"old" aquadopps (1400 serie) using the V1.23 deployment sofware. I received my "new" aquadopps ( 1600 serie) with the deep water deplyment sftw, where there is no advanced set up page , and which give different predictions for energy and standartd deviations  from the V1.23.
can I use ANY soft for ANY currentmeter, or which combination is the best?
Thanks for fast reply , we go to sea in a week time ....
Herve