No, you can't co-mingle funds.
They don't pay tax on per diem because they write the amount off as an expense.
You're treated differently as an employee (W-2) than as Self-Employed (1099).
Since you are now working a a contract worker, you are Self-Employed.
Since you did not setup an LLC or other business entity, you will need to file Schedule C.
Schedule C is part of Form 1040 but you will need to purchase TurboTax Home & Business (Desktop) or TurboTax Self-Employed Online to file.
Schedule C is where you will report your income as well as your expenses, like Meals and Travel.
Because you're not an employee, you also pay your FICA tax (Social Security/Medicare) this way.
If you are working/earning in North Carolina, you will need to file a North Carolina State return and pay tax on that income.
HERE is a link with more information
HERE is a link on North Carolina Filing Requirements
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