If you want to create a new View programmatically you should generally instantiate it in your View Controller using its designated initialiser:
UIView *testView = [[UIView alloc]initWithFrame:myFrame];
If you create a custom view it's totally fine and correct to put some configuration code in the init method, but it's your ViewController that should be in charge of deciding what to do with this view - it is his job! Using the MVC the View and the Model should never communicate directly (as you definitely learned in the first lesson of CS193P).
Therefore the same apply to the animations. You should animate the Views within your ViewController and not implement the animation in the View itself.
Therefore in my opinion you "second position" should be setup by the VC - if this has to be done when something happens to the view (e.g. someone pressing a UIButton) you should set a target/action to your VC and handle this within your VC.
ADDED: Regarding building UIViews in the Interface Builder I don't know what you mean by "and let them go". Interface builder will create the views and add them to the specific superviews at runtime - as you can see in the example below you control the view hierarchy graphically on the left. For instance in this case there is a UIView (which I coloured green for clarity) and two buttons. One is a subview of the main view while the other is a subview of the green UIView.
Once your ViewController is loaded the view hierarchy is automatically loaded to self.view - in fact if you run the following code in your VC when it is loaded you will see the list of self.views subviews in your console.
for (UIView *view in self.view.subviews){
NSLog("%@", [view description]);
}
If you know already that you need to change some attributes of a specific UIView you setup via Interface Builder (e.g. we know we want to change programmatically the color of the green UIView in the example above) you should create an outlet which allows you to have a reference to that view in your code. You do it by crtl-drag from the storyboard to your ViewController code - see the example below.
When you have done that you can refer in code to this as any other property, with the difference that it has been created by Interface Builder.
Hope this helps.