How do I link a .sks file to a .swift file in SpriteKit

This method will unarchive an sks file and initialise it as whichever SKNode subclass it is called on. This means you can unarchive a file as an SKNode (so the root node will be an SKNode) and add it as a child to your scene. You can also unarchive a file as GameScene or any SKNode subclass.

extension SKNode {
    class func unarchiveFromFile(file : NSString) -> SKNode? {
        if let path = NSBundle.mainBundle().pathForResource(file, ofType: "sks") {
            var sceneData = NSData(contentsOfFile: path, options: .DataReadingMappedIfSafe, error: nil)!
            var archiver = NSKeyedUnarchiver(forReadingWithData: sceneData)

            archiver.setClass(self.classForKeyedUnarchiver(), forClassName: "SKScene")
            let scene = archiver.decodeObjectForKey(NSKeyedArchiveRootObjectKey) as SKNode
            archiver.finishDecoding()
            return scene
        } else {
            return nil
        }
    }
}

Use it like this:

let scene = GameScene.unarchiveFromFile("GameScene")! as GameScene

or

let levelStuff = SKNode.unarchiveFromFile("Level 1")!
self.addChild(levelStuff)

By the time of this answer (Xcode 8.2.1) the 'simple' way of doing this for scenes:

• Select the .sks file in your Project Navigator so the Graphic Editor is displayed
• Go to the Utilities Area (on the right hand side)
• Click on Custom class tab (icon looks like a contact card)
• In “Custom class” enter the name name of the class in your .swift file