Notes vs. comments
Use notes to record thoughts that only your colleagues can see. Use follow-up comments to talk to a scout about one of their specific entries.
Mission Notes vs Follow-up Comments
When viewing a scout's entries inside a mission, just click the "notes" tab at the top right to write a note. Scouts do not see notes, and are not notified about them. (You can also write notes about a specific scout's application in a screener.)
Scroll down to the bottom of any entry to write a comment that's sent to your scout. Depending on their settings, scouts are either sent a push notification or an email that one of their mission leaders has sent them a message.