Using a Cookie Cutter to Make a Design

I'd probably do what you suggested - which is to trace the other shapes on top of the iced cookie. You could do this with a food-safe marker, or score the outline into the icing with a tip of a scribe tool or turkey lacer. If you didn't want one color on top of the other, you could also use the smaller cutters to score those shapes into the bottom cookie before the cookie bakes. Some impressions would be left after baking, which could then be used as a tracing guide to lay colors side by side.

I hope this helps, and is what you were after!

Yes, most of the time I will be using the lines impressed into the cookie, which is good.  But for some things, I think it's just easier to flood the whole area and then pipe on top of it.  I do have a scribe tool, so I will do that.  I just wanted to make sure there wasn't some miracle answer out there that I hadn't thought of!

if the bottom level is only one color, you could do it in fondant and make the indentations on the fondant.  Now you have the lines for your icing.  Good luck.