I would probably free feed til at least 12-16 weeks. You wouldn't want to come home to a shaky pup. Then you could feed on whatever schedule you choose or continue to free feed.
If you want to crate train later, it probably wouldn't be a good idea to put a pee pad in the crate. That might send mixed messages.
Something that could work for you is getting a very small crate and keeping the door open. Then around the crate put an xpen. So in the xpen would be a pee pad, food, water and crate. That way the dog isn't eliminating in the crate, so you might be able to use it for training later. Did I explain that okay?
And I think if you ultimately want to train your pup to go outside, it is best to start that way. Pee pads could confuse it but if it works best for you then use them.