I am a believer you have to do what works best for you I free feed all my dogs and it works for me. I had very good luck with the pee pads for training. And I would just restrict the area where the pee pads are the litter box is. Until they learn this is the proper place to potty. Running the whole house does not help you potty train. mine always potty after playing or waking from a nap Even when you free feed they pick a certain time they eat. At least mine do. And the best advice is to be consitstent and if you do potty training will be over before you know it. You both are just getting use to each others body language. Pretty soon your 12 week old pup will have you perfectly trained
good luck and stay positive it will be well worht it