To get back to this thread, it seems that editing the default *HCTOSYS_DEVICE 
*field in /etc/default/hwclock won't work in my situation. I'm assuming 
because the RTC1 (DS3231) is loaded via a script when Debian boots the 
hwclock has already loaded and defaulted to RTC0 because RTC1 is yet to be 
loaded.

This isn't really too much on an issue though. Using Adafruit's guide for 
creating a script 
<https://learn.adafruit.com/adding-a-real-time-clock-to-beaglebone-black/set-rtc-time>to
 
load the RTC (DS3231) I am able to set the system time and default hwclock 
RTC0 on bootup. Likewise I have made a similar script that runs when Debain 
shuts down, reboots and halts to set the DS3231 RTC to the system time. 
This allows the system to sync with an NTP server if available and update 
the external RTC.

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