Complications arise for standoff annotation when the annotation is not on the source text itself, but on a more abstract representation. This is particularly the case in a language such as Arabic with morphological and orthographic challenges, and we discuss various aspects of these issues in the context of the Arabic Treebank. The Standard Arabic Morphological Analyzer (SAMA) is closely integrated into the annotation workflow, as the basis for the abstraction between the explicit source text and the more abstract token representation. However, this integration with SAMA gives rise to various problems for the annotation workflow and for maintaining the link between the Treebank and SAMA. In this paper we discuss how we have overcome these problems with consistent and more precise categorization of all of the tokens for their relationship with SAMA. We also discuss how we have improved the creation of several distinct alternative forms of the tokens used in the syntactic trees. As a result, the Treebank provides a resource relating the different forms of the same underlying token with varying degrees of vocalization, in terms of how they relate (1) to each other, (2) to the syntactic structure, and (3) to the morphological analyzer. 1.