If a template is well built you don’t need to clear the channel everytime after you show it. Stopping the template should leave the layer fully transparent. So the question here is why do you need to clear the channel.
I do not fully understand that question. As far as I understand you are talking about a preview with a burned in time-code, right? If that runns on another channel you would need to feed that channel to the ATEM also to make it available for the multiviewer.
Problem here is, that the ATEM’s (until very recently) do not support macros or such stuff. You can use Companion or JustMacros to do that. There are also some GPI solutions around, see this thread.