My trick to using array collections is a custom made PHP class that while transmitted through AMFPHP behaves as a native array collection, instead of an array.

When I create the array tree in PHP, before passing it to Flex, I convert each array node to ArrayCollection using this class:

class ArrayCollection {
	var $_explicitType = "flex.messaging.io.ArrayCollection";
	var $source = array();

	function ArrayCollection( $array )
	{
		if( !isset( $array ) )
		{
			$array = array();
		}
		$this->source = $array;
	}
}

Usage would thus be:
$node = new ArrayCollection( $myarray );

Hope this helps.