Long john in a freedive suit means that there are straps over the shoulders and a little extra on the chest, and yes it's underneath the top part of the suit.
The advantages of long waist pants are that you can easily take a pee at the shore or on a boat without taking the top off, and you might breath a little easier.
Any freedive suit should be bare open neoprene on the inside, especially in the climates you (and I) are in. Don't get a suit that has nylon or cloth or even sprayed on metalic lining. Just bare 'open-cell' neoprene. You will need to lube the suit to get it on and off, but it's worth the slight extra effort.
Custom fit, which is cheap in freedive suits from Europe, is worth the few $$ extra. Trust me
Peace,
Erik Y.
