[Lizard]

(Disclaimer: I'm a test pilot, not an engineer, but I work a lot with the engineers.)
Yes, we use XCode (and Subversion -- you'll want some sort of source control, even if it's just you). I've heard somebody (or maybe a few somebodies) recommend Aaron Hillegass' book, "Cocoa Programming for Mac OS X".

As far as getting the "feels natural" part right, it's about learning your audience. If you are the only user, you can just try out each change you make to your app and see if you like it. But if you hope other people will also find it natural, you'll want to follow User Interface guidelines (such as Apple's HIG) to help your app behave similarly to other applications. You'll also want to get someone who either is a potential real user (or is similar to the users you expect) to try it out and give you honest feedback. What is natural to you may prove to be very unnatural to them.