I received short term disability from a third party. I did not receive a W2, the IRS has in on file and want to know if I should amend my taxes to include this and how.

how do you know taxes were withheld, if you didn't get a tax form? generally if tax was withheld you should have gotten a tax form. There would be no reason to withhold tax on a nontaxable payment 

amounts paid by an insurer attributable to premiums paid by an employer that were not included in your taxable income are taxable

payments attributable to premiums you paid including after-tax contributions to an employer's plan are not taxable as well as employer-paid premiums included in your income.   

"The IRS has it on file"  how do you know they have it on file? Does this mean you received a letter of correction?  If so, the letter would have told you what you needed to do.  It may have said they wanted you to amend your return or that you needed to do nothing if you agreed with the changes and if you did not agree it would have told you how to dispute the income.

Was this a policy paid by your employer?  If so, then it would be taxable.  If you paid the premiums for the policy, then it would not be taxable and not need to be included on your return. 

Was there a W-2 issued that you can contact Mutual of Omaha to get? You should contact them to see what records they sent to the IRS. 

If the IRS has already processed your return thoroughly and did not make any corrections, then you can Amend Your Return.  Otherwise, follow the instructions in the letter or wait for them to finish processing your return.