Since you say you are new to cooling so I wouldn't suggest doing anything high end like buying a custom cooler/waterblock for your GPU but what you can do is buy a good GPU with a nice cooling solution say a Twin Frozr/Direct CU and Ice Q kind of stuff.
Another thing you can do is add more case fans to your case and do some cable management to optimize airflow.
And what do you mean by "how to set em up in a micro atx system"?
If you mean how to install a GPU then you just have to plug it into the PCI-e slot and connect a few powercables.
Also if you do wan't to go extreme and install liquid cooling for your GPU then you can buy waterblocks from dangerden and other brands.
In a decent case, no additional cooling is really necessary with current GFX cards, especially the non-reference designs like the Asus DCII series, MSI PE series, etc.
An micro ATX case on the other hand is by definition small and limited with regard to cooling. OK for a single card, non overclocked but I wouldn't advise OC'ing the GFX card or doinG SLI / CF in such a small case w/o doing something special.
Personally, I consider a mid tower with good cooling essential for single card systems and full towers for SLI ? CF systems.