Different Dog Training Methods in the same home?

I am looking at getting a puppy very soon. My room mate already has a 2 year old dog of his own. He taught his dog the basics using a reward/punishment training method. She has developed some bad habits such as jumping on couches that frankly don't bother me but things I would not want my dog doing. I have been researching clicker training and plan on using this method. My questions is whether his dog's bad habits will affect my puppy's training. Will I be able to effectively teach my puppy not to do the things his dog is doing or would it be a lost cause?