Ok, just looked at your gallery pics. I "think" your helm water issue may be from the side panel meeting point. If you look at your starboard side pic, where the helm horn is, that's where the panels meet, and it some may be coming in through there. Depending on the amount of rain, up front, it may be also be coming in at the cleat cutouts.
When these covers are on, they shed A LOT of water .... think of a downspout .... a temporary help when calling for bad weather (once you are dried out) is to put some backer rod in some of the gaps underneath. It's a closed cell foam backer used in wide joints before you caulk. This might help to narrow down where your issue is coming from. (Don't keep it there permantly, as the gap allows air movement and drainage if excessive water gets in)
http://www.amazon.com/dp/B001OBTZ1E
Also keep in mind if your toon sits level, or "bow down" ever so slightly all the water rolling onto stern deck from cover, will want to go forward.
If it's not already, try to get it sitting "bow up" at your dock, so the water sheds off the rear deck "to the rear".