If you have a graphics program capable of editing .dds files (Photoshop with the dds plugin is what I use, Gimp has one, too I believe) you can add your artwork easily. You could set each artwork up as a JSGME compatible mod and activate which ever one you wanted. You would have to put the artwork on each type of submarines conning tower graphic, though, if you wanted it to work no matter what type of sub you had.
As far as the killflag boats go, if you like one of the designs on one of the boats we have created, then you could download the skin for that boat and just not send in update reports. That way, you would have the design, but wouldn't have the killflags.