Arnie:
Simple answer: No.
Although it is possible to have the OS running on the eMMC and an application located on the uSD card, I would highly recommend that you do not try to do it that way. Life will be much easier if you have your application and the OS in the same location.
So, choose either the eMMC or the uSD card as the location for the OS and the (SoftEther VPN Server) application.
Install the OS and get it running.
I highly recommend you have a serial cable on the serial console port for all of this.
SoftEther VPN Server for the ARM is provided as source code, so you will need to make sure you have all the prerequisite tools and files installed, then use the “make” procedure provided with the source code to build the application on the target beaglebone.
It also includes some self tests to make sure the build works and is compatible with the target hardware.
Then you will need to use the command line to start the VPN server.
Then, you will need to use either the Windows or Linux console configuration tools to configure the Server.
It is possible to write a service.d script to automatically start the VPN server whenever the beaglebone boots, but these files are not provided as part of the Softether distribution.
So, I would say that this effort is not for Linux or Beaglebone beginners. You need to have sort of medium Linux skills to pull it off.
It works real well once you get it going. Both the Beaglebone and the SoftEther VPN Server are extremely stable
— Graham