Thanks to user Trayal:
To anyone who is interested, I was able to get this to work through custom commands directly by adding the following to my profile in profiles.conf
.
CustomCommandPath="ccextractor\ccextractorwinfull.exe"
CustomCommandParameters= -wtvmpeg2 "%sourcefile%" -o "%destinationpath%\%showname%_S%season%##E%episode%##.srt"
CustomCommandHangPeriod=0
CustomCommandCritical=true
CustomCommandUISession=False
CustomCommandShowWindow=False
You’ll need to customize the parameters to match your naming scheme, as necessary.