Some dog learn more quickly than others.  Some might pick it up in a matter of weeks, but more often than not the process can take many months.  It sounds like what the puppy has learned is that when you say "what did you do" she should run to the wee wee pad and it makes you happier, but I doubt she realizes that's the only appropriate place to go.  Dogs don't have a very good memory when it comes to things like that and she will not associate your stern voice to the accident unless you catch her in the act.

First off, in general using potty pads will make the process much longer than it has to be because you are making it okay for the puppy to go potty inside initially.  This can be confusing to them.  After all, carpeting is like one big wee wee pad only it's more comfortable for them so they are more prone to using it.  I would highly recommend crate training.

For crate training for the purposes of potty training, get a crate just large enough for the puppy to stand up and turn around.  Some puppies can handle more space and not have an accident, but if not, this will eliminate the opportunity to go potty on one end of it and then sleep on the other.  The key is not to crate them all the time, but it should be used if you aren't home or can't keep an eye on them.  When puppies are very young or even adults who have never been potty trained, they need to be let out about every 2 hours, 15-20 minutes after eating and right after any spurts of excitable play.  they should always be praised immediately after they go potty outside either with food or attention depending on what makes your dog happier. 

When inside the house, it's best to keep the puppy on a leash at all times at first.  This will create an "umbilical cord" and you will be able to keep a closer eye on your puppy and even learn more quickly the signs she gives just before she goes potty.  Especially now that she is used to going potty inside, it's important not to let her run off out of view until you guys develop a better potty routine.

After a little while you will be able to let her off leash more, but make sure to only do it when you know she won't pee such as right after you come in from going potty outside.  Prevention is key.  When you do have an accident, make sure you clean it up as soon as possible after they happen with an enzymatic cleaner like Natures Miracle to make sure you are really getting it clean.  You may need to clean it multiple times and may want to try a carpet cleaner/steamer.  After it's cleaned properly you should no longer smell anything in the house.  The fact that you can is also not helping your puppy.  Because the smell is in the house, she is less likely to understand why she can't go potty inside since she already smells it.  To make sure you get it all, you can buy a small blacklight, turn the lights off and shine it on the carpet.  If your carpet lights up like a hotel room on CSI then you need to clean it again.  The blacklight will show you any hidden remnants that you may not be able to see or even smell without it.  Your puppy, however, can.

You will need to be very diligent at first, but using all of these methods you should find that your puppy picks it up very quickly.  Good luck!