If I undestand correctly what you're asking:
- you cannot transport troops using sea regions that contain enemies (showing as red when you press v)
- if you want to attack a faction by invading from sea, and they have ships in one or more of the sea regions that you need to use to attack them, you will be unable to do that, although they are neutral; their ships act as a guard, and prevent any invasions to be launched at them through the sea regions in which they are present; you need to either sink them, or use another route; of course, if they are neutral, they will only prevent you from attacking their own provinces, not others (you can attack Italians if Sicilian ship is present, but you cannot attack Sicilians themselves); this is also useful when you need to protect your own coastal provinces from surprise invasions