I have to apply skins to my app and I am wondering wat is the best way to do this. I'm not asking about techniques to implement them, when they all are packed inside app. I'm asking about options to add additional new skins (png,xml files) when my app is out no App Store. I can achieve this by adding an upgrade to my app, but this will be painful for those users who don't want new skins, they will still have to download the upgrade. Any solutions?

Having your app download png and xml files from a server you run sounds like a simple solution for what you want to do, though you might need to be careful about Apple's guidelines when doing so. From memory, it should be OK if you're not downloading executable code, but I haven't read the agreement recently.