
All the bodies systems slow down at night so not much urine is produced but initially the bladder is tiny[walnut size in an 8 week old dachsie so I have been told by a vet] till it stretches when control of sphincters is achieved and more urine can be held therefore stretching it.
My pups sleep by my bed so as soon as they move I am up taking them out with no fuss or conversation, starts off being about 2am and gradually gets later, the light mornings I cover their crates so they don't think it is getting up time at 4am. As they get older and start to sleep through you may have times when they lapse so I will take them out,if it becomes a regular thing I try telling them to settle down and usualy they do,if not then I take them out.
I give all my dogs get a dental chew at bed time, the pups start off with an appropriate biscuit for age/size.
I had the same problem re water being tipped over so found a system similar to how rodents get water but bigger in Poundland one day, you attach any size plastic drinks bottle up to 2 litres and train the dog to use that [mine were adults and learnt very quickly and taught the pups by example] I bought 10 packs but was too generous and gave all but 2 away to friends, when one got chewed I took ages to find more but did find them on Ebay in Hong Kong, much dearer but worth it. I now don't have to worry if the water got knocked over just after I left the house or just before I returned. There is a bowl of water outside for normal drinking so the bottles are not their only access to water, 5 dachsies in a large puppy pen have access to 2x2litre botles which are freshened up twice a day and if during seasons or illness someone needs to be isolated then they will get their very own bottle.
There are other systems but they tend to drip if you don't get the right vaccuum in the bottle which defetes the object,my system has a spring behind the ball so stopping the drips and comes apart for cleaning when required.
Will go find link to drink system.