When fitting new pads on used rotors the last thing you want to do is "panic stops" from the get-go, you should ride the bike and use the brakes gently but frequently so they bed in to the profile of the rotor without getting hot....this is the proper way to do it and how I was taught and it works.

Warped rotors can be caused by corrosion build up under the rotor mounts and around the mounting bolt threads.

Make sure all is well in that area before mounting new rotors and if they need attention it has to be done at a machine shop or you will completely munt the next set of rotors.

If it was my bike I would pull it apart and double check just in case you warp those new rotors.