A good steam cleaning would probabaly be the best solution..... and once it is cleaned..........
Stanley Steemer has some spot cleaner that works pretty well....... the best thing you can do for Pee Pee accidents is get to them as soon as possible.... if the spot is diluted with water first and then soaked up with a towel... it helps. There is also a machine that is available called a "Spot Bot" that is suppose to do a pretty good job and there is a cleaner by bissel that you can use in it that is for pet stains ( My daughter used one when her "pound puppy" was being potty trained and seemed to think that it worked well)
Maybe confining the puppy to one area when you are unable to watch her for "gotta go pee pee signs" would help, too.
Good Luck!