I have not done it myself, but if you search on the board (use the search box upper righthand corner of the screen) you should find several threads on the topic. Try searching on variations of "wedding signature quilt". Here is one thread I found that may be helpful to you:
http://www.quiltingboard.com/main-f1...t218797-2.html
A couple of tips I have picked up. (1) Iron freezer paper to the back of muslin fabric, then cut out your squares. Freezer paper adds stability to the fabric. It's probably best to cut these squares oversize also (an extra inch on all sides). (2) Instead of drawing seam lines on the fabric, get some file folders and cut out a square the size of the signatures you want. Mount the freezer-paper backed muslin inside the file folder with this cutout space showing. This way guests will keep their signatures inside the square and not go into your seam line. Hopefully you can find these tips explained better in some of the old board threads.
Edit: I would test all of this out, include the pens or markers you choose, before preparing the quilt. Wash your test squares several times to make sure the marks are sufficiently permanent.