Retirement tax questions

"Will the IRS know who I nomineed EE bond interest to,as you cannot put in their SS#?"

No.  There's no provision for that.

"
Do you just change box 3 to reflect the total amount on the recipients return? "

No.  You simply enter the amount you've that shouldn't be included in your income tax return in the "nominee" questions that come up after you enter the 1099-INT.  That amount will be shown as a subtraction on your Schedule B.

Tom Young