Not a specialist subject for me i'm afraid but i believe that mating a 16v to the original gearbox is easier than changing the whole lot due to different selector linkages required and work required with drive shafts etc hence why the 8v box is still in your car. As far as getting the one you have out, its not something i'd want to do on my own for the first time by reading a guide.
You'd need to do things like support the front of the car on axle stands so the wheels have no weight on them, strip everything thats gonna get in your way, engine cables, pipes etc. remove drive shafts from hubs and gearbox because i dont think the mk2 16v driveshafts are any use, you would need late scirocco or cabby shafts which have the larger 100mm inner cvs, they are the correct length and have the correct outer cv for the mk1 hubs.
You could swap the drive flange on the mk2 16v gearbox to take the smaller mk1 90mm inner cvs. This way you can use your existing mk1 driveshafts. You'd probably need a pump jack to support the engine and an engine crane to support the box when you've undone everything or vise versa. I'm sure all the detail for dropping you're current box out and putting 1 back in is covered in a haynes manual.