How can I change the position of alerts pop up? With Yosemite we got handy, growl-like, alert popups from the notification center. It's great but it often hides handy utils which also take the top right position of the screen.

Is there any way change the position of those alerts (via system preferences, plist, or an app)?
Unfortunately, there is no built-in way to change the position of the popups still. Problem is well known (for instance, see here: Change location of notification center alerts).
The only way you can customize the position of notifications is to use commercial app - Growl (http://growl.info) for those apps that support it or turn all or some notifications off via System Preferences -> Notifications.