Lori, you do need to use a different type for embossing. Look for the kind that's meant for laser printers. Since laser printing requires heat, this type will stand up to the heat of embossing.
As for "archival" ink, that just refers to its resistance to fading. It is not the same thing as "permanent" or "solvent" ink, such as Sharpies have. If you think about it, pens/inks meant for use with transparencies are intended to be non-permanent, so you can wipe them off easily.
You want something more permanent than that.
Staz-On for the stamped image, Sharpies to color in; that should do the trick! You could also try regular acrylic paint, or paint with Pearl Ex added for a pretty sheen. Dye inks, though, will not work.
Make sure and post your creations! We love to ooh and aahh, lol.