If you only need to file form 5329 and aren't required to file a full tax return, you can just file form 5329 alone, but this is probably uncommon. For example, if your only income is non-taxable social security, and you need to file form 5329 because you missed your RMD and want to request a waiver, you can file it alone. But if you have other taxable income and need to file anyway, then form 5329 will be part of your finished tax return as an attachment to your form 1040.
I believe you can enter an explanation in Turbotax when you get to that step, although someone else who has used the program for that function might have a better idea of the exact steps. Unfortunately, you can't attach extra documents like PDFs to a Turbotax tax return, that's a programming choice. But some forms do allow a written explanation.
