How do I make a dock for a shuttle on a custom submarine? Instructions for both the main sub and the shuttle part would be appreciated. Thanks.

Far as I know you need vertical or horizontal docking bay for your shuttle, same goes for the submarine you want to use it with. You can find them both in the Editor's misc section. Once you have both your custom shuttle and submarine in functional condition, wire both their docking bays with button (toggle), so that it can be detached/reattached either from the sub or shuttle. Then open up your main submarine that you want to pair the shuttle too. In the editor's top middle section it displays a tab labeled "Add submarine" it'll show a list of shuttles and subs. Select the shuttle you want to use in that list and it should appear as a boxy outline with a +

To pair the shuttle's docking bay with your sub's you must select the Shuttle and then while holding space click the Submarine's docking bay to link it, if done properly it should now have a red link to each other.

Then all you have to do is save and then test it out in the game to see if it's properly setup. Remember to make sure the hull and spacing of door/hatches are done so that while docked there is no gaps that would cause flooding in between the dock ports when they open.