Thanks! I'm glad to hear that switching to the pine was easy. I really don't want to have stinky puppy pads in my house. I bought the SoPhresh pellets as we really don't have any space to store 40# of equine pine. We use feline pine for our cat but are able to get it in reasonably sized bags, and I really love how they work.
There are SO many reasons not to use puppy pads. I'd switch sooner rather than later. I would NOT use "So Phresh" or other compacted paper, however, for two reasons. One is that it is so absorbent that you can't tell where they have peed, and it can get surprisingly odiferous. Second, the pellets stay whole and expand... alarmingly. I would worry that a puppy who swallowed some could end up with a BAD impaction if the swelled inside them. I tried them once and would never use them again. They scared me!
If you get a 5 gallon covered pail from Lowes or Home Depot, it will hold MOST of a bag of pine pellets. If you set up two litter boxes, you will use up the rest.
I also would not put puppy pads or anything else that the puppy thinks of as a potty surface over the entire bottom of the pen. The whole point is to teach them that some places are OK to potty, and others are not. If the breeder has done a good job, they should already have a good idea of that in an ex-pen-sized space. You want a surface that is waterproof and easy to clean under the ex-pen, not something you EXPECT them to soil. I've found a vinyl floor remnant of appropriate size is perfect.
As far as MOVING the whole thing every night... I wouldn't! That's a LOT of work, and the puppy doesn't need that space overnight, when he should be sleeping. Get a small crate (which you will need anyway) and put it beside your bed, where you can stick your fingers through to comfort him if needed. If he cries during the night and you think he needs to potty, be gentle, but all business. No play, no cuddles, take him to his potty, put him down and tell him to potty. (which he won't understand at first, but eventually he will learn the signal) Give him no more than 2 minutes. If he really has to go, he'll do it in 30 seconds!) Then put him gently back to bed.
Depending on whether the breeder has worked on crate training with him, he may fuss and cry a bit the first couple of nights. (though none of mine did) You can put your fingers in the crate to comfort him, but don't get into "conversations. A quiet, cheery, "Go to sleep" (or whatever you want to say) is all you SHOULD say. Depending on his age, he MIGHT need to potty once or twice at night for a week or two. By 12 weeks, almost all puppies are sleeping through the night.
We have a litter box in our bedroom, tucked between the dresser and the wall for the (very rare) times that one of ours needs to potty at night. In an apartment, you might not have stairs to navigate half-asleep, into the MUCH COLDER part of the house. So it might be convenient enough just to carry the puppy to the living area litter box at night. That's up to you.