Are you talking about the path that shows up in the dialog when the user is installing the app? Even though it says "C:\Program Files\" it doesn't mean that your app will be installed directly in the "Program Files" directory. It's actually asking for a location in which it will create another directory to contain your application. So for example if the user chooses "C:\Program Files" as the "installation location", AIR actually installs the app in "C:\Program Files\<app name>". For instance, when I installed TweetDeck I left the "installation location" as "C:\Program Files" but TweetDeck is actually installed on my machine in "C:\Program Files\TweetDeck". (I personally think that's confusing, and I know there have been some discussions about this internally in Adobe, but I don't know if anything's going to come of those discussions.)
Nevertheless, if you want to change the default intall location you can do that. In your application config .xml file, you specify the default installation location in the <installFolder></installFolder> node. Whatever you specify is a subpath of the default install location, so for example if you specify "<installFolder>Workshare</installFolder>" in your application.xml file, the installer dialog would show "C:\Program Files\Workshare" by default. However, assuming the user didn't change the install location, and assuming the app is named "MyApp", the app would actually be installed in "C:\Program Files\Workshare\MyApp\". I suppose that's useful if your company makes multiple apps and you want them to all install in a single subfolder of the Program Files directory, but otherwise I don't think it's what you're looking for.
I'm afraid I don't understand your question about the certificates. I'm not sure what you mean by an "Adobe Certificate" or a "Private Certificate". The basics of certificates are that you need to have your app signed by some certificate in order to distribute it. You can create your own "self-signed" certificate, but unless you give the user a copy of your certificate and they add it to the set of trusted certificates on their computer, their computer won't trust the certificate. Consequently, when the user installs the app they'll just see the "Publisher: Unknown" in the installation dialog. If you buy a code-signing certificate that's issued by a known certificate authority, then the certificate will probably be trusted on the user's computer so AIR will show your name as the Publisher in the installer dialog. It's basically a reputation system. Your computer trusts Verisign (or other CAs). Verisign says that your certificate is legitimate (because Verisign issued the certificate) so Verisign is saying "this person really is who they say they are". Since Verisign vouches for you and the computer trusts Verisign, AIR can legitimately say that the app really comes from you.
For in-depth details about certificates and code-signing in AIR, see the Dr. Dobb's Journal article "Code Signing in Adobe AIR" by Oliver Goldman (the AIR engineer who led development of the installer).