
Your first night was perfect!! :) so I would continue with that routine for the next couple of days and then gradually knock the getting up during the night altogether.
IMO, the second night where you had tired him out before bedtime and he had then woken you up several times, you take him out for a 'wee' and he only wants to play, he had actually got over excited before bedtime, and because you had got up to him each time he had barked, he had got wise to this and if you like 'played on it' :) I am not slating you, I know how difficult it can be to have a pup sleep peacefully through the night, and there are so many different ways that people deal with this situation, but in my experience I have never had my pups upstairs with me, ONE because if you eventually want them to sleep downstairs you are infact IMO, making more work for yourself in that you would have to get him used to sleeping back downstairs anyway, and TWO the most important, a Bernese pup should not be climbing up or down stairs at a young age due to their soft bones, so keeping him downstairs in his den is perfect.
I had a Bernese pup that would bark the first couple of nights I had him, I did like you and gave him a covered hot water bottle, soft music, cuddly toys etc: he did settle after a couple of days of me ignoring his wimpers and barks, I did go down and let him out for wee, ignoring him etc, but soon realised I was being woken up for company instead of wee duty!! So I stopped getting up and within a couple of nights he settled great!! :)
So hang on in there, what seems like he's getting worse, will work out all ok. :)