It's going to take them a little while to adjust to the new smells etc but there's no reason why, eventually, they won't be completely unbothered by the puppies so try not to worry.
Our rabbits are outside so things are a little different as they don't tend to interact as much but, when we first brought our cat home, they behaved in a similar way - they seemed very uneasy about the different smell, the first few times they actually saw the cat they would run and hide etc. They did eventually get used to her presence though, although still behaved the same way when we brought our first dog home for the first week or two. But the smells would have been different of course and the dog is about 50 times bigger than our cat. :lol::lol:
Like joybell said, they do eventually get used to the different noises/barking etc too. My two don't even bat an eyelid now if Kane barks or if both dogs are play barking/growling out in the garden. Likewise, if the dogs go up to the mesh to have a sniff, the rabbits usually have a good sniff back and don't really seem bothered by their presence at all.
For now I'd let them get used to the smell. Maybe let the puppies sleep on a blanket or an item of clothing and then place that somewhere in/near their enclosure so that they can investigate it in their own time and then gradually introduce them to each other once they seem less bothered by the smell.