Last year was our first year on DBA P/R and W-2's.  We were working through a lot of problems, like only part of the year being DBA etc.  So I'm a little fuzzy on how I actually accomplished the whole task.  My notes will be better this year!
 
I think the way I handled Non-Cash wages was through payroll.  In this case they were for automobile usage.    The auto usage is increased by the amount of the taxes to be paid (mandatory stuff only: medicare, ss, city tax, 401K)  I estimate those amounts and keep adjusting the pay to get it right.  If there are a few cents left over, just put them in federal tax or state tax.  If you need to record them in fringe benefits, setup a pay category that posts to fringes.    
 
To get close to the gross wage amount, add up the % of the deductions, subtract from 100%, divide the result into the non-cash benefit.  
 
The wage amounts are adjusted properly.  The only downside was that I had to manually type on the W-2 in block 14 "AUTO ALL" and the amount.  I did not have to go in and adjust the other parts of the W-2.