Have a single owner llc. Wife has written several business checks to our sole employee as salary when I'm unavailable to generate payroll check through our intuit pro w/enhanced payroll software. Just learned of this. Now faced with what to do about it. Certainly want to be able to deduct payment for services. Can I generate a 1099 for these monies? Or other solution? Any help greatly appreciated.

Salary needs to be paid regularly on a schedule. If checks were issued in advance of a salary, they should be deducted from payments. If it is too late to deduct from 2014 salary, then do it from 2015. But this does not appear to be 1099 income.

What do you mean 'deduct payment for services?'
Salaries are basically wages, with federal and state taxes deducted, and payments such as UI made by the company, and reports made to the respective agencies on a timely basis, possibly quarterly in your case.
If you go an entire year of sometimes just 'writing checks,' you are in a quagmire. W2s have to be finalized and printed and postmarked or handed out in 3 days.

If you mean you want to issue a 1099, not legal if the employee didn't meet several criteria, then feel free. But he will be paying self employment tax as well as income tax on it, probably with no deductions, so your wish to deduct his pay as an expense takes second place. It isn't fair to him. He can turn you in to the IRS. You can be flagged for an audit.

An IRS payroll audit isn't pretty.

How much in W2 wages was paid, and how much in misc? (Your wife needs to stop being allowed to write checks and you need to start keeping an eye on your business.)