I have a pair of padded under shorts (a bit like female boxer shorts that are padded) from Corrine Dennis, which I really like. In the winter I wore these under a pair of altura winter tights which are not padded. I find the padding in the under shorts good because they don't have any of the ridges which so far I can't seem to get on with. I also have a pair of Pearl Izumi and Ronhill cycling shorts, but I prefer the Corrine Dennis ones. For protection at the moment whilst I am breaking in my new B17, I will wear the padded under shorts and a pair of the padded cycle shorts on the top, so double the protection.
Ideally though, I think I would prefer not to wear padded shorts at all and I am hoping that when my saddle softens a bit I will be able to do this.