First of all, you need to be a level 4 guild with 20k GP to spare. Once you do this, you will need to speak to the guild merchant (think that's what he's called) and buy a guild emblem scroll.
Then, you need to come up with an image. It needs to be saved as a 24 bit BMP file that is 16x16 pixels. Microsoft Paint will make it easy to do this.
Once you have the image, you will need to put it in a certain location. Go to your C Drive, then Program Files, then Silkroad. Save the image in the Silkroad folder. Be sure to check that the file is saved as "guildmark".