In my experience it has to be one or the other. Not both.
Pad training/litter box training takes due diligence and can be done while using crate training as a means of control until it is time to go, just have no pads or bedding in there (except perhaps a white towel, if you notice it's being pottied on outside of the schedule you're trying to set, then your pup doesn't get any bedding at all.). And instead of taking your puppy outside, you take them to the pads, which I usually advise...especially for boys...is that you place your pee pads inside a large size cat litter box so he/she has to make an effort to get into the box before eliminating thereby eliminating accidents on the edges of the pads and creating a mess on your floor. Some males will get half in and half out before going pee. If that happens, you can raise the litter pan just another half inch off the ground to ensure they get all the way in.
There are plenty of ways to get done what you'd like to get done.
Feel free to e-mail me (faster response) anytime.
topsredhead@yahoo.com
~Leslie