I am quite skeptical about the use and usefulness of ecosystem accounts for larger regions with diverse ecosystems. You might wish to check out a recent article on "Do we need ecosystem accounts"

(Ecological Economics .Online: http://dx.doi.org/10.1016/j.ecolecon.2014.12.026)

There have been some developments in this area in last ten years and mostly by the European countries. The methods to do this are largely three separate areas of research:

a) extending system of national accounts (SNA) that has now been extended to develop System of Environmental-Economic Accounting (SEEA),

b) develop segmented  system of accounts for natural bio-diversity and/or corresponding impacts for example one developed in the Netherlands - NAMEA - which can capture change across periods, similar to that of SNA for economic activities,

c) develop combined form of accounting for example ENRAP,, also known as Perkins framework.....

Theoretical modelling associated to these developments can also depend on PIOT framework as well as use MFA analysis. I am not sure if it helps you, but you can start looking into articles by Hoekstra & van den Bergh (2006), Pedersen & de Haan (2006), Rout, 2010. 

Hi Micheal, you might wish to check 

European Commission, Organisation for Economic Co-operation and Development,

      United Nations and World Bank (2013), System of Environmental-Economic

      Accounting 2012, Experimental Ecosystem Accounting. Online:

      http://unstats.un.org/unsd/envaccounting/eea_white_cover.pdf. My critique (in the previous answer) refers to this publication).