We recently pad trained a small shih tzu. He has a playpen but it is about 6 ft long. His bed and toys , water are at one end and the pad was at the far end. It worked well for us. I really do not like to use potty pads but he was small 2 lbs and was sick. It worked very well for us, when he wasn't in there we put a pad on the floor near where he was. He always used it. Now we have transitioned to outdoors mostly. We will put the pad in the playpen as the is where he sleeps at night because none of us were getting up. He now holds it and no longer uses the pad. I take them all away now during the day as he will go outside. I will only put one in if I leave for an extended amount of time otherwise he thinks they are too fun and shreds them up. What you don't want is the pads to be too close to him, he needs space that is clean for him otherwise he won't learn. They naturally want to be clean and sleep where it is clean.
First, what do you mean by "let?" Do you mean you mean you just assume that the puppy will occasionally have an accident, and the pads are there to contain the mess? Or that peeing/pooping in the xpen is going to be standard practice?
To my mind you should start as you mean to continue. I personally do not use pee pads in the xpen. First, I don't use them for adult dogs. Therefore, I don't want to habituate the puppy to peeing on soft surfaces. Second, I don't want my dog peeing indoors, period. I don't want the dog peeing in the xpen, the kitchen, or any place else where he can look up and see ceiling. That means taking the pup outside frequently and crating him when I can't watch him. Finally, puppies have a tendency to turn pee pads, bedding, and everything else in their xpen into toys. I would rather not have to clean up shredded bits of pee pad.
Of course, I have a yard, an uncarpeted room where I can put the xpen, and a spoo. I might feel differently if I had a small dog in an apartment on the 19th floor.
If you want him to use the pads, put them in the same corner. Personally, I would use newspaper, but do not leave newspaper around where the dogs can use them. If you train them to newspaper, you can always put the newspaper down (presumably outside) where you want them to go. Easier clean up. And, if they are nervous about "going" in a strange place, they will go on the newspaper you put down.