Step1: We assume that you have installed the plugin as specified here
Step2: Please visit Settings->BuddyPress->Settings( Or if you are on Multisite WordPress Install, Please visit NetworkAdmin->Settings->BuddyPress->Settings) as shown below
Please click on the Settings tab on this page as shown below:-
At the bottom of that page, you will see the settings for BuddyPress private Message Rate Limiter as shown below
Please put the settings you want there. Have fun!