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I haven't found it to be too difficult at all. You do need to clean the environment as well as treat the puppies. This is because the infected pups and dogs shed the cysts in their fecal matter. When rain or other water washes over the fecal matter, the cysts are washed into standing water. Dogs and puppies drink from the standing water and become reinfected. So it is important to clean up all fecal matter. You will need to bathe the pups and dogs to remove any cysts on the fur. The area they are in should be disinfected with a bleach solution of 1 part bleach to 10 parts water.
I personally routinely disinfect my yard with a bleach soluton to prevent the spread of disease since we have a large population of uncontained dogs and cats in my neighborhood.
For actual treatment of the puppies there are a few treatments that are used including Flagyl (Metronidazole) and panacur. It sometimes does take multiple course of treatment to clear and sometimes concurrent treatment is used for stubborn cases. You can read about these below.
You can read more on giardia below.
Be sure and practice good hygiene as this can be spread to humans. This is why it is very important to teach children to always wash their hands after handling or playing with puppies. If you disinfect well and isolate and treat the pups, clearing up the giardia shouldn't be too hard. I did forget to mention that dogs that swim and play near creeks and in lakes can contract it from those bodies of water as well.
Some people do find it hard to get rid of giardia but I've found that they have generally missed a body of standing water or their dogs have come in contact with another dog or their fecal matter that may have caused reinfection.
I hope this information is helpful to you.