How to file taxes when short term disability is taken into account?

My fiance tore his acl over the summer and is having surgery next week. He filed for fmla and short term disability. He will only be on disability for 6-8 weeks. When he filled out the paperwork it asked about tax with holding on his disability checks. He checked no because for some reason he thought it meant taxes would be taken out, but I explained it to him and so now we will have to pay those taxes at the end of the year. How will we file taxes at the end of the year, since we won't be having taxes taken out for those 6-8 weeks?
    You will get a form at the end of the year.  I don't know what you will get, maybe a 1099 or something else.  You enter the income on your tax return along with everything else like W2s, interest, etc.  Then you will either have a tax due or a refund on your return.  If you want to pay some ahead of time you can make an estimated tax payment so you won't owe so much on your tax return.  If you owe too much you may pay a penalty and interest.

    You must make quarterly estimated tax payments for the current tax year if both of the following apply:
    - 1. You expect to owe at least $1,000 in tax for the current tax year, after subtracting your withholding and credits.
    - 2. You expect your withholding and credits to be less than the smaller of:
        90% of the tax to be shown on your current year’s tax return, or
      100% of the tax shown on your prior year’s tax return. (Your prior year tax return must cover all 12 months.)

    Go to….
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    Form W-4 and Estimated Taxes - Click the Start or Update button

    Here are the blank Estimates for 2012 and instructions…..

    The 1040ES quarterly estimates for 2012 are due April 17, June 15, Sept 17 and Jan 15, 2013.  Your state will also have their own estimate forms.
    • Taxes owed may depend on State program.

      "Are state short term disability benefits taxable?  Only five states have a disability program in place and the answer differs for each state as the manner in which premiums are paid differ.  
      California state disability insurance benefits are not taxable unless your benefit is in place of unemployment insurance.  The premium is 100% employee paid via after tax deductions.  California SDI also funds the CA Paid Family Leave program which is considered unemployment insurance and thus is taxable.  

      New Jersey temporary disability is funded by both employee and employer contributions.  Therefore the benefit is taxable, but only in proportion to the contributions made by your employer.  The taxable amount should appear on your W2 statement at the end of each tax year.  NJ temporary disability benefits are not subject to New Jersey income taxes.  

      New York state short term disability premiums are partially funded by employees and employers.  Benefits are considered taxable in proportion to the employer and employee contributions.
      Rhode Island temporary disability benefits are not subject to federal or state income taxes."
    • I figure since they asked him if he wanted taxes taken out then it jwould be taxable.
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