I have a small trailer that came with a 14ft vhull jon boat. I also have a 12 foot vhull Jon. In order to get both boats to fit well on the trailer. I need to move the crank mechanism gizmo in the direction of the wheels. This will let the end of the 12 ft boat sit flush with the end of the skids, but now the 14ft boat will hang off the skids about a foot or so. The skids are at least 3ft long.

My question.....is it OK for the back of the boat to hang off the skids and how much is too much.

Right now when the boat is on the trailer, the front of the boat is very close to the vehicle. I am thinking that if I move everything back to where the boat is centered more over the wheels then I would have some space between the hitch and the boat and that would aid in backing and launching. The weight of these aluminum jon boats is not very much and the distribution over the wheels looks like the way it should be rather than the transom directly over the wheels.

The trailer is one of those little Harbor Freight things for boats from 12-14ft. It does a good enough job and came in the deal. Here us a link to a pic of it on the HF site. http://www.harborfreight.com/cpi/ctaf/displayitem.taf?Itemnumber=5002 I just noticed in the HF pic, the piece that you secure  the front of the boat to is positioned way more towards the wheels than mine is. It is easy to unbolt and slide.

Any advice is welcomed.

The boat should be positioned on the trailer so the tongue weight on the trailer is at least 10% of the total weight, some say 20% but I've never run that much tongue weight and never had a problem with sway. If the tongue weight is too light, or hitch is too high, you will have a problem with the the trailer swaying.

The bunks/skids need to extend all the way to the transome and just a little past to fully support the hull. You may cause a hook in the hull if the transome is not support.

So, get you tounge weight right and then install longer bunks if needed to support the boat.

Thanks for the advice.  I went ahead and set it up so that the bunks stick out about a foot with the 12ft boat and the 14ft boat hangs over the bunks about a foot.  Best I could do to get the trailer to serve both boats.