You will need to use the manual override billing amount field for the labor you don't want profit on.

Sorry I should have also included where you do that. 

On the job cost records, T&M tab.  So basically you compute the T&M, preview it, drill into the labor you don't want marked up, use the override option, save the change.  When you have updated them all, recompute.

Well, I'm not talking about the Billing amount. The billing amount is fine.  I'm talking about the markup/profit calculated on that billing amount - what we call the "Builders fee."  This is set up in 3-10-1 - which calculates a builders fee based on Cost Type.  It's possible to calculate (or not calculate) a builders fee on ALL labor for that job - but I want to charge a builders fee on SOME of the labor costs, but not others. 

I don't know if this is true for everyone, but our cost type 2 is for labor.  What I need to do is be able to assign a DIFFERENT cost type to particular labor costs - which you can do for vendors, but SAGE doesn't allow you to do for labor.  If you go to the job cost input screen from entering payable invoices at 4-2, you can assign different cost types.  But if you go into the job cost input screen from entering payroll, Sage doesn't give you the option of changing the cost type. **   You CAN change it in the actual job cost record at 6-3, but this doesn't help, because then it no longer recognizes it as labor and it won't calculate the billing amount based on hours.  Nor will those labor job costs show up on labor reports.   **It's funny that if you go into a job cost record from the journal transaction payroll makes (1-3), you can see the cost-type column, but you cannot change it.  

Basically, Sage needs to allow more than one cost type to labor.  I need a 2nd cost type for labor so that I can assign a different 'markup/profit/builders fee' value to them.   

Well, I'm not talking about the Billing amount. The billing amount is fine.  I'm talking about the markup/profit calculated on that billing amount - what we call the "Builders fee."  This is set up in 3-10-1 - which calculates a builders fee based on Cost Type.  It's possible to calculate (or not calculate) a builders fee on ALL labor for that job - but I want to charge a builders fee on SOME of the labor costs, but not others. 

I don't know if this is true for everyone, but our cost type 2 is for labor.  What I need to do is be able to assign a DIFFERENT cost type to particular labor costs - which you can do for vendors, but SAGE doesn't allow you to do for labor.  If you go to the job cost input screen from entering payable invoices at 4-2, you can assign different cost types.  But if you go into the job cost input screen from entering payroll, Sage doesn't give you the option of changing the cost type. **   You CAN change it in the actual job cost record at 6-3, but this doesn't help, because then it no longer recognizes it as labor and it won't calculate the billing amount based on hours.  Nor will those labor job costs show up on labor reports.   **It's funny that if you go into a job cost record from the journal transaction payroll makes (1-3), you can see the cost-type column, but you cannot change it.  

Basically, Sage needs to allow more than one cost type to labor.  I need a 2nd cost type for labor so that I can assign a different 'markup/profit/builders fee' value to them.   

You might want to add a calculation and include it via paygroup. This gives you granularity to Job and employee type (pay position). Add the calculation(s) to the benefits for that paygroup, they can be employer cost type calculations.