you probably know this already, but the basic rule for instantiation is something like
protected function my_function():void
var my_list: List
my_list = new List();
my_list.id = "my_list";
Setting the id is prtty much essential if you are going to refer to the new object somewhere later (if it's just some static text, you may not want to bother).
the above should work whether you're in an MXML file or AS - you just need to get the import right each time you use it.
But maybe what you are meaning is not the instantiation part, but that the new object does not function as expected?
In your class you may need to do explicit imports of classes that are otherwise automatically available in MXML. Post code and give more details on your issue.
My first impulse is that you're missing imports somewhere. although that should cause compiler errors. Do you see any?
My second is that you're not creating an instance of the new class and invoking the method on it. Just because the class exists does not mean it will be compiled into the final SWF; you still have to create an instance and call methods on that instance, or if a Static method, call the methods.