I have never used puppy pads - I didn't want Lottie to think it was acceptable to go inside the house.
She has a small crate in my bedroom, but the bigger crate downstairs which like you, I brought so it can be used when she is an adult if required, has been partitioned off. She is nearly 18 weeks, but still a dinky thing, and has access to about half of it (it's a 36" crate) - big enough for her to stand up, turn around and stretch out. She doesn't get left in it for more than a couple of hours at a time (and that's maybe happened twice) - she is in there for about an hour in the morning between me leaving for work and daycare picking her up, and again an hour (if at all) in the evening, if they dorp her off and I'm not home yet (most of the time our arrival coincides). But she was fine for a couple of hours last week when I was held up returning from a meeting in London. She just sleeps TBH!
I had a divider provided with my big crate, but you could do the same with a box.