The GPS antenna is easily located under the dash board in that case. So long as it has line of sight up through the windscreen then it will work fine through the dash and the glass so long as their is not metal in the way.
If you look at http://www.mercupgrades.com theres a document about installing comand (which is what was in W208 clk) - and one about installing comand-aps into a A/B class - the W209 clk install is very similar to that (same antenna, and loom, but beware CLK comand-aps part number is different and you need the right comand-aps unit!!) , the dismantling of the dashboard is referred to in the old comand document - although on the CLK you can pop out the upper switch panel by opening the coin holder and hooking your finger round and pulling it out !