Hi, this is just going to take patience and consistency. Its very common behaviour so don't worry.
Depending on how you feel about crate training, i ALWAYS use this method for house-training and have found dogs will be clean within 1-2 weeks.
However, if you don't wish to use that method then i would strongly suggest you forget the paper training method. This only forms yet another habit to break. Take up the paper. Routinely feed your pup. You will find (if you haven't already) when they tend to go. Regularly put them out to go to the toilet. Praise is really key. So as soon as they go to the toilet praise like mad. If you know they are due to go, but haven't, don't allow them back in until they have. REmember to praise.

If they come inside and wee, don't show any emotion, just pick them up, take them back to the spot, point to it, say very loudly 'no' (holding and looking at them) and immediately put back outside (staying with them observing). They may not go again but just give them a few minutes to make the connection and bring them back in.
Keep this up consistently.
The crutial thing is to remove the paper. This only confuses the issue and keeps their scent within the house. Plus, of course, you're almost giving permission to go inside.
In regards to overnight, try to keep them in an area that's 'easy clean'. When you get up if they have done anything, again showing no emotion, do the same pointing method and immediately put them outside. Eventually they will get into your routine and be ready and waiting for when you get up.
Hope that helps
