Depending on your notification settings you can set who the notification is sent from.
For example many of my custom notifications can go out from me and they look like this in the recipients Email:
matthew @ cirrusops.com (via QuickBase) <notify@quickbase.com>
Then the replies will come to me. However, if the notification is not specified who it is from and just says
notify@quickbase.comAny replies will be lost is space.
If you want any replies to come to a specific email, you can add that email as a user to the application (make sure they are withing your domain's "Company") then add them as the sender in the notification.
After it is send, you can bring those emails back into an "Inbox" table within your app through a variety of sync/integration options with your mail service.