The general rule of thumb is that puppies can hold it their age in months plus 1 hours. So unless Daisy is way, way younger than she looks in the picture you posted in the Christmas present thread, she doesn’t need to go out at 3 and 6 am. Her nosing around for ages before getting down to business would seem to bear that out–if you need to pee badly enough to get up in the middle of the night, how long do you typically spend twiddling around in there before you actually go? A lot less than 15 minutes, right?
Right.
I would highly recommend crate training her. The benefits are legion. It speeds up the potty training process, as nobody likes to eat and sleep in the bathroom. It gives her her own enclosed space, which is something dogs tend to instinctively seek out due to their natures as den animals. You don’t have to worry about her chewing shit up while you’re gone. It gives you a safe and psychologically comfortable place to put her if you’re working on something messy or hazardous or have allergic people over. And if she ever needs hospitalization or boarding or has an injury that requires cage rest, she’s not freaking out over being in a cage. That last is a huge deal for a lot of the animals I work with–we’ve got several patients that have to be sedated the whole time they’re with us, or else they shriek constantly or rub their noses raw on the door, or stress themselves into a nasty case of diarrhea. And many of the owners worry themselves sick over how the pet is responding to the cage. It’s easier on everybody to just crate train 'em.
Something else I would really recommend is handling her feet, mouth, and ears every single day. That way you can trim toenails yourself instead of taking her to the vet for it, and clean her ears, and give her pills, and all that jazz. At some point she’ll probably need ear drops, or eye ointment, or have a cut on her foot that needs cleaning, and your life will be infinitely simpler and more pleasant if she’s used to being handled in that way.
And since she’s a border collie, she’s going to need some sort of mental stimulation. Dogs are like kids, when they get bored they tend to get up to mischief. The smarter the dog, the more easily it gets bored, and border collies are very smart. Puzzle toys are good, as are Kongs filled with frozen peanut butter, agility training or flyball.
On preview (I’ve been fighting with the damn computer for ages trying to get it to take my post), I see that you are crating her. Trust me, messing in her crate and having to sit in it a few hours isn’t going to hurt her any. It will be much harder on you than on her. In fact, it will help her make the association that this is gross and I really ought not do it. Also, if you cut out the middle of the night walk, she’ll be more likely to go in the mornings because there’s more likely to be some urgency.