The portion of the stipend that is not used for qualified educational expenses may be taxable. to deteremine the amount of income tax you would owe, you would need to calculate which tax bracket your in. If you are a student employed by the school where you are pursuing a degree as a full-time student, you wouldn't be subject to the FICA tax, only income tax on the stipend.
If the employer is a W-2 employer, they should be withholding your FICA tax and making the payments on your behalf each quarter. If you are not receiving W-2 wages, then yes youwill want to include FICA as part of your estimated tax liability on that income. Here is a good resource for calculating estimated payments.
You can make estimated payments directly to the IRS by these methods.
Hope this helps!
Cindy
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