I've got three opinions from three different instructors I've had when it comes to signing. One is don't, ever. The next is to sign the mat board if dry mounted, or if not dry mounted and there's enough border on the print, and the border will show through the window of the top mat, sign in the border with pencil only, signature bottom right and edition or date bottom left in the border of the print so that it shows through the top mat and is not covered (so that the pencil won't smear to the bottom of the top mat). The third, who is a definate post modernist, thinks a fat sharpie marker (or equivilent) in the print area itself, on the front, is best, even if it discolours, etc..
Personally, if I have to sign a print, I use a Staedtler pigment liner pen, and sign the border of the print, bottom right, but I mat so that it's covered. The pigment liner is archival and very, very perminant, and I've yet to see it transfer to the top mat even if it gets wet, seems to write on just about any paper I've ever used as well. I don't like pencil, smears to easily and doesn't always like papers without a surface tooth.
Gerald