If you want her to learn to go outside all the time you should remove the papers. BUT you will have to extra watchful and not let her out of your sight. If she continues to wander off and have any accidents in the house that will confuse her and mess up her training.
When Chester was little I would set a kitchen timer for 2 hours and take him out every 2 hours even if he didn't act like he really needed to go. I called these the "preemptive potty breaks" and it helped him get used to always going outside. Also, as soon as he would start to peepee I would say "Go potty" and within 2 weeks he had learned to peepee on command.
Don't worry. You will be fine. You just have to be extra watchful and take her out a little more often until she is 100% trained. Good luck!
"My little dog: A heartbeat at my feet."