Most of my pants have a smaller pocket sewn into the right front pocket (like some dress pants have, I don't know what that little pocket it called), it allows my to carry a folder clipped inside my pocket, and still within easy reach (my Paramilitary and Endura fit perfectly).
I haven't had any problems with clips showing, but I have seen a few raised eyebrows when too much of the knife is showing (that's why I love my SERE's deep carry clip!). Most of the time I wouldn't mind, but at the university I've found it wiser to carry anything larger than a SAK concealed.