If you are running the Create Profile command with the Drainage Network Reference = Existing Profile, then yes, that command projects the network defined in the From/To fields to the existing profile. This is the correct way to show crossing pipes, because crossing pipes will only display when you display a network profile. If you do not want to see the projected pipes, you might want to consider giving those pipe a feature style that will display the projected pipes on a level that you can turn off.
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