Hi Adam
There are many clever options
Two points to remember
1 Martin is right that a through transom pick up would not work underway as it would be dry at speed, pump would burn out and/or bait dies
2. any skin fitting underwater should be metal and be fitted with a shut off valve in case a pipe goes
Have you any acces to the inside of the main hull, if so that may be where to fit the skinfitting.
Charlie