Re: how far off bunks
good suggestion for balancing there. I guess you need to pull the boat up with it a foot back (scary!) since you need to do this on level ground, or pull the boat back a foot once you are level.
BTW i was at the marina today, and with this thread in miond, noticed all the big boats on lifts with big outboards, many twins, hanging more that a foot or two off the bunks on the lifts. Didn't hear many "Crack! Ker-splash" of transoms falling off so I moved on.
not that scary, you do it when picking up the boat so you just don't winch it all the way in and you keep it connected to the ball and you lift up on the tongue with it still attached and you can tell the weight that's on it and stop when you think its getting close, then release the hitch at home and feel the weight as you dial it in. if you think you went too far and have too much weight on the tongue then loosen the bow rope, back up and stop quickly to shift the boat back an inch or so. for large heavy boats its best to do this at the launch with a lift so they can help adjust and balance the boat for you. you never want more weight on the tongue then you can lift by hand or its unsafe and dangerous.
the trailer axle and suspension is designed to carry the weight of the boat not your truck so if its tongue heavy the suspension cant work correctly and when you hit large bumps it lunges forward instead of upward because the suspension is not at the correct angle. this also causes the back of the truck down and lifts on your front wheels causing potential loss of traction and control.
you just want enough weight on the tongue so it stays securely in place when you hit bumps, you don't want the truck squatting or the trailer tongue leaning downward. the trailer should be flat and level.
as to the launch seeing boats like that, maybe they are set like that so its easy to hook up the lift straps because the strongest part of the hull is at the transom so trailering them on the road like that is asking for trouble but I doubt any boat will just crack open but over time it will warp the hull if its not supported properly.
naturally you adjust the weight on the tongue for the size and weight of the boat you have so jon boats I would put about 50-75 lbs, for bay boats up to about 19ft I would go about 100-150 lbs, and for larger bay boats up to 25 ft with tandem axles I would go 150-200 lbs. anything larger then that or for heavier boats its best to get the recommendations from the trailer manufacturer so it carries the weight correctly for the way the suspension is set up.
EDIT: after the comments below I did more research and found bay boats are a little heavier then I first accounted for so I adjusted my numbers upwards slightly to reflect that more accurate weight. the weight of a lightweight trailer (under 2,000 lb) doesn't matter when calculating trailer tongue weight but if its a heavy duty I-beam trailer then add 25% of the trailer weight to your boat and motor weight and figure 10% of that (a number smokeonthewater agreed with until I said it and it was then somehow wrong lol) is going to be very close to the numbers I quoted. in most cases your rig wont fall apart if the trailer isn't balanced properly but tire wear, handling, and gas mileage will suffer.