People who are fully disabled are allowed to take disbursements from their IRA or similar account without the 10% penalty for early withdrawal (before age 59-1/2). Form 5329 is how you take that exemption.
Some financial institutions will look at a physician's statement or other documentation of your disability and then issue a 1099-R, others (like mine) do not
Do not add anything to a paper filed return when mailing it ... the data input operator will not even look at it so just keep it incase you are audited.
I'm not sure what you're saying about the 1099-R. You will get a 1099-R for any IRA distribution. If the distribution code in box 7 of the 1099-R is 2 there will be no 10% penalty and you do not need Form 5329. If the distribution code in box 7 of the 1099-R is 1 you need Form 5329 to claim an exception to the 10% penalty.
In any case, as Critter-3 said, do not include any additional documentation with your tax return. If the IRS wants additional information they will send you a letter asking for it.