If you only have one domain controller and it is Virtualized on Hyper-V, what is the proper way to configure Windows Time?

First, make sure time sync to the host machine is turned on in the Integration Services. 
Next, on your Domain Controller add the following registry key:
reg add HKLM\SYSTEM\CurrentControlSet\Services\W32Time\TimeProviders\VMICTimeProvider /v Enabled /t reg_dword /d 0
This ensures that the domain controller only syncs its time from the host OS when being restored from a saved state.

Next, inside the guest, run the following commands from an Elevated command prompt:
1.net stop w32time
2.w32tm /unregister
3.w32tm /register
4.Net start w32time
5.w32tm /config /update /manualpeerlist:"0.pool.ntp.org,0x8 1.pool.ntp.org,0x8 2.pool.ntp.org,0x8 3.pool.ntp.org,0x8" /syncfromflags:MANUAL
6.w32tm /config /update
7.net stop w32time && net start w32time
8.w32tm /resync /rediscover

Line 1 stops the time service
Line 2 Completely removes all time settings from the registry - you may have to run this twice, or you may get an access denied.  If you get an access denied, just run it again.
Line 3 Re-creates the Registry Settings
Line 4 Starts the service
Line 5 Sets the server to sync with the NTP servers pool.ntp.org
Line 6 Updates the configuration
Line 7 Restarts the service so the new settings take effect.
Line 8 Syncs the clock to your new NTP servers.  - This needs to return "The command completed successfully."  If it does not, something went wrong with one of the steps above.