Two Companies, One Payroll, All salaried employees - How to allocate job costing correctly

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Sage only allows us to enter hours per employee per job.

Example:
Salary at 5,000/mo (paid through Company 'C')
Time sheet entered as 20 hours goes to Company 'C' and 40 goes to Company 'A'
Job costs is incorrect because 40 hours goes into  Company 'A'
Sage is set to only read the Salary.
Then it takes the 5,000/mo and divides it by 20 (since the 20 is part of the Company 'C')
Therefore the amount of the 40 hours is posted through Sage to Company 'A' and cash is transferred from Company 'A'  to Company 'C''s bank account.  
This thereby reduces the "overhead salary" (in Company 'C')
How would we correctly job cost in each company if the (Salaried) employee is working in both Company 'A' and Company 'C'?