COPs? Boot? What?

When I bought my car (99 GT) it had a misfire, took it to my mech, he replaced something on Cyl #3. He said it was a COP, but someone else told me he only replaced the boot. Does replacing a boot fix a misfire, or did he really replace the COP. his is my first Stang so Im not too sure how all this works. Can someone explain the diff between these. Also, Im doing a tune up, what is the benefit of replacing the boots only. Is there any? or should just do the COPs???? Best place to get either besides dealership??? Thanks

Thanks for the excellent reply. Well Im takin it in tommorow again, Ill have the mech take a look at the COP. Thanks.

By the way, are the COPs replaced until they go out(like a sensor would), or routinely(like oil filter would) Thanks