I enter per diem slightly differently.  I use a Payroll Calculation (5-3-1) labeled "Per Diem".  After all the hours are entered on the timecard screen, I switch to the "Calculations" tab and enter the Per Diem using the Payroll Calculation I created.  I enter a flat amount for the week and it's posted to the JOB/SHOP/OvH/Admin expense account that I set up in the Payroll Calculation.  This allows me to post the per diem to the job or shop, etc but keep it separate from the Labor cost.   

When you do it that way you are not able to job cost it appropriately.  When you use the pay type peri diem on the timecards you can job cost to a specific job and it fills in the per diem calc on the calculations tab. If you only use the calculation then it divides the per diem between all jobs on the timecard which typically isn't correct 

I should have clarified, our non-union construction company per diem is a flat amount per day and all employees receive the same per day amount.  Yes, my method divides the per diem between all jobs on the timecard but in our case, that typically works.  Our crews work on projects for weeks at a time so usually don't have more than two jobs on a time card.  The only time it doesn't work is when they received per diem for one project and not the other.  Our per diem cost is usually 1% or less than the total job costs.  Management decided that being able to separate per diem from labor was more important to them than knowing the job cost for per diem might by be off a few dollars.  If employees are working on several jobs in one pay period and some have per diem and some don't, then our method would not work.

I should have clarified, our non-union construction company per diem is a flat amount per day and all employees receive the same per day amount.  Yes, my method divides the per diem between all jobs on the timecard but in our case, that typically works.  Our crews work on projects for weeks at a time so usually don't have more than two jobs on a time card.  The only time it doesn't work is when they received per diem for one project and not the other.  Our per diem cost is usually 1% or less than the total job costs.  Management decided that being able to separate per diem from labor was more important to them than knowing the job cost for per diem might by be off a few dollars.  If employees are working on several jobs in one pay period and some have per diem and some don't, then our method would not work.