I spent years doing this the wrong way - using the parts store/aftermarket pads, just jamming them in until they fit, only taking the rotors off when they were completely shot... long story short, I ended up re-doing all my brake jobs at least once a year because one side wouldn't be gripping the rotor at all, the other side would be ground down unevenly, etc. Here's what I've learned:
- If the rotor can be re-used, remove it and have a parts store machine it to give your new pads a fresh surface to bed in to. If it's too worn down, replace it. Either way, put a thin coat of anti-seize on the wheel bearing surface when you put the rotor back on.
- Take your caliper slide pins out, clean them and their channels with brake cleaner, and lubricate them with a silicone-based grease like SYL-GLYDE. Petroleum-based grease will cause rubber to swell, and that can cause the rubber bushings in the slide pins to stick.
- As cerbomark said, take a wire brush, a file, whatever will fit into the caliper bracket, and clean the caliper bracket where the pads/clips sit.
- When reassembling, make sure the clips sit snug in the caliper bracket. If you can't get them to seat all the way, keep sanding the caliper bracket down until they seat properly. Use an appropriate brake parts lubricant on the channels where the "ears" of the brake pad will slide in and out.
- OEM pads typically don't have fitment issues at this point, but many cheap parts store pads do. Once you get the pad into the caliper bracket, it should slide evenly in its channel. If only one end of the pad wants to slide, and the other end wants to stick, it may be necessary to sand the "ears" of the pad down a little until it fits into the caliper bracket and can slide evenly in the channel.
I live in salty New England, so I typically re-grease the pad channels and caliper slide-pins at least once a year.