Adjusting to the palace or any other cage environment does not always happen immediately, that is part of the reason we designed the loft to be easily cleaned. Be sure you puppy eats, drinks and eliminates before bedtime. You might try moving the loft to the other end of the cage or placing a foam bed on the loft.
Getting a puppy to eliminate on a pad takes time and repetition. With outdoor training the puppy has things to do and a large area where elimination is okay so it is easy to comply with the rules. Restricting the elimination are to a couple square feet with nothing to really attract or occupy the puppy makes it more difficult for the puppy to get the idea. The only way is to repeatedly place the puppy on the pad whenever you are home, place him on the pad after eating, drinking, playing or sleeping.
If he starts to eliminate elsewhere pick him up place him on the pad so that he can finish in the right place creating the opportunity for praise. Having the pad in a small collapsable pen keeps him nearer the target. Pee pad attractant sprays occasionally help also.