I'm not sure how you're appending it to the body, but for showing you how to do it I'll assume it's just an element you have.
var newPaneElement = .....
someOtherElement.append(newPaneElement);
In order for your directive to be processed now, you'll have to tell it to $compile
You can do this by running the following directly after appending it to someOtherElement:
$compile(newPaneElement)($scope OR scope);
I put $scope or scope because I'm not sure if where you're appending it is in a controller, or within a directive.
If you can paste a jsFiddle that would be helpful.
There's no need to do compile, I think you should watch some of the tutorial videos on how to use angular. Looking at the jsfiddle you have, you don't need jquery. Also you have a directive wiring up on the pane element, but then within that directive you have another pane element so it was doing a recursive loop and crashing. I've fixed the fiddle up to do what you need:
JsFiddle http://jsfiddle.net/BcvPz/1/
Use an ng-repeat and then you can just have pane elements repeat wherever
JsFiddle http://jsfiddle.net/BcvPz/2/