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It depends. There are a few advantages to having a separate payroll account.
First, you may not want employees knowing your company's primary checking account number.
Second, if your primary account is ever overdrawn, but your payroll account has been funded, you don't have to worry about a payroll check bouncing, which would be very bad for employee morale.
Third, you can put "payroll account" on the payroll account checks, which might make it easier for an employee to cash if that's what they do.
Having said that, I've seen lots of large companies that don't use payroll accounts.
As for which account you use to pay the taxes and other things, I am not sure that matters. I suppose one could argue that you should run all payroll related items through there.
I'm a business owner, not an accountant -- but my answer would be yes, you probably should. It can help avoid legal, regulatory, and security issues. Also, payroll is essentially an accrual account that has a large balance variation every pay period. In addition, if you're doing payroll yourself, a separate account makes it easy/faster to reconcile the disbursements (i.e., it's immediately obvious if there are lost, stolen, or forged paychecks). Finally, if you have certain types of withholdings and payroll deductions (like 401k contributions), I think it may be required.
For internal control purpose, I recommend a separate account for payroll. This account should be use just for paychecks. While preparing the payroll, the tax liabilities should sit in your liabilities until a check is drawn from your regular checking account.