When building a new application, start by creating a 32-bit MPLAB Harmony 3 project in MPLAB X IDE by selecting File > New Project. Chose the Configuration name the based on the BSP, and select the appropriate processor (e.g. ATSAME70Q21B). 

In MHC, under Available Components select the appropriate BSP, such as SAM E70 Xplained Ultra. Under Bluetooth->Templates, double-click on BM71 Bluetooth. Answer Yes to all questions. 

You should end up with a project graph that looks like this, after rearranging the boxes:

There are no MHC options for the BM71. 

You can also bring in the BM71 Driver by itself, by double clicking BM71 under Bluetooth->Driver in the Available Components list. You will then need to add any additional needed components manually and connect them together.