Two Historical Data Items (HDI) will be needed:

1.  The first is an Earnings item that you'll enter a timecard for. 
History type:  E
Calc order: 0,
Entry type: Amount,
Rate from:  none,
Basis for:  Enter .e fica and .e ficamed in field 4 Basis for of the earnings HDI. This will calculate these two taxes (employer portion).

2.  The second HDI will pull in this Earnings HDI as a deduction - thus creating a $0.00 check. 
History type:  Deduction,
Calc order:  500 or 700. 
If posting to the GL, it will be best to post this to the same GL account the Earnings HDI were posted to. 
In field 8, line 100, create a REGOP line loading reg 2 with the current amount of the Earnings HDI .  
It will look like this:  reg(2) op(L) item(HDI name, cur, amount). 

The system defined 941 columnar payroll report pulls in the employee .fica and .ficamed wages.  It may be necessary to modify this report to also pull in columns for the .e fica and .e ficamed wages.  Copy the 941 report to a second report name and pull in the employer portions - because it probably won't fit on one page. 

Again, it would be best to review this with the auditors - but it appears it is possible to issue two W-2's for the employee - one for regular wages and a second for the 3rd party payments.  Creating a second employee number might make this easier to reconcile / report at year-end.  Any HDI set up as an Earnings type will pull into the W-2.  Depending on the type of reporting done for this on the W-2, it may be necessary to edit them at year-end.