My first question is, how does the IRS know that these withdrawals are contributions and not gains? When I withdrawal the funds does it trigger something at my brokerage (Fidelity) to send me a specific tax form about this?
Unqualified distributions from a Roth are assumed to take place in this order:
1) First, contributions and rollovers made more than five years ago
2) Then, rollovers of less than five years ago, in the order they were made
3) Then earnings.
You don't start taking any distributions from Bucket #3 until Bucket #1 and Bucket #2 are completely empty. So, your initial withdrawals are almost certainly going to be mostly from contributions, and will be non-taxable.
I called Fidelity today to ask them for some guidance but they made it sound like these withdrawals are between me and the IRS. I can move the funds from my ROTH to my Brokerage but it was, "up to me to clarify that I was withdrawaling contributions with the IRS." Is this really how it works? Is there some separate form I have to submit saying "in 2012 I contributed $5000, I'd like to withdrawal that now."?
That is correct; it's on you to report this to the IRS. And yes, there is a form. On Form 8606, Part III, you will enter your "contribution basis". (That's Bucket #1 above.) Then you subtract your distribution. If you still have contribution leftover, then it's assumed that your distribution came from the contributions. Only when your contribution basis drops to zero do you start taking out earnings.
This sort of leads to my second question, my brokerage (Fidelity) only has my statements back to 2011 (10 years), so I only know my contributions for those years, but I know I have contributions leading back to some point in the late 90's. Does the IRS know this somehow or do I have to rely on past statements that I didn't save from over 20 years ago? I'm guessing the answer to the first question is the same answer to my second question....
Yeah, you're going to have to research what your contribution was. Remember, to the IRS, you only have one Roth IRA. Multiple accounts, multiple brokerages, whatever; it's all the same IRA when you report your taxes. Good luck!
Caveat: The above applies to unqualified distributions, and assumes you've had the Roth for five years. If you're over age 59.5, then it's all free. Also, this does not apply to "corrective distributions", in which you do distribute earnings. And it goes without saying, this is general information which may not apply to your specific situation; consult a qualified tax professional for advice.