I don't know how you could effectively use a scooter to penetrate a wreck where there are alot of corridors, rooms, small spaces, etc...What is suggested is to anchor the line right inside the entrance point. You go several feet and wrap the line around something to form another quasi anchor, go a few feet more and do the same thing and repeat the process until you get to your destination. It is also a good idea to put some strobes or light sticks at a few points. If you have a silt out they won't help alot until it settles out some. When you leave you reverse the process. It's also a good idea to have a diver at a couple of points along the way.
There is also the school of thought relating to "progressive penetration." This is where you progress into the wreck a little at a time to get completely familiar with where you are. On subsequent dives you progress a little further. You end up so familiar with the wreck that you do not need a reel to penetrate. Places like subs where the spaces are very small, you will run the risk of the reel line getting you into an entanglement situation and progressive penetration may be the best way to go.
There is also the school of thought relating to "progressive penetration." This is where you progress into the wreck a little at a time to get completely familiar with where you are. On subsequent dives you progress a little further. You end up so familiar with the wreck that you do not need a reel to penetrate. Places like subs where the spaces are very small, you will run the risk of the reel line getting you into an entanglement situation and progressive penetration may be the best way to go.