"in May 2020 he contributes $6k post tax into traditional IRA"

Stop here. Do you know which tax year this is contributed for? Did you get the 5498 from mid-2020 for tax year 2019 from the client?

"Not really following how 5498's drive the contributions as that's money in."

That's where you start. Nothing you stated makes it clear that you Confirmed you have 2020 over-contributions. You only described Distribution activity.

Have you confirmed if the May 2020 contribution is for tax year 2019, paid in by the tax return filing due date, which was July 15th of 2020? Did you get the 5498(s) for 2019 and for 2020 (and for 2019 it might have been re-issued as Amended late in August)? That's how you determine which inflows belong to which tax year.

As @rbynaker  pointed out, May 2020 could have been against 2019 tax filing year and Dec 2020 could have been Fine for 2020 and just Earlier than this client typically funds their retirement. A client who always waits until their tax return is ready, to fund their retirement account for the tax year being Filed, needs to know to get the Amended 5498 later that year, and give them to you. Did you ask if they typically wait, but decided to work with you Dec 2020 in advance of their 2020 tax filing prep?

You might not have any over-funded condition at all.

"If i have 2x 1099's showing $12k into IRA's - is that not a problem for the IRS?"

No, there is no Problem here. If there had been two conversions from the same broker, there would be 1x 1099-R. There will be as many 1099-R as there are brokers where funds were taken Out, and the amount(s) can be $12 or $1.2 million. It's just money Out. It's just Information. It's your job to show on the tax form if there is further action taken.

Let's review "backdoor" Roth:

You don't qualify to contribute to Roth, but that's where you want to invest, so you put a Nondeductible post-tax amount into a Traditional IRA account. The intent is to use the Back Door to sneak money into a Roth.

At some point, you Convert some amount to Roth. It doesn't have to be right away. Even if it is, it won't be considered the exact same money. It's only considered to be the same money, when there are No Other Accounts that are Traditional IRA or other deferred type.

It won't be a taxable conversion if you have no other funds in any other deferred account (or, only basis in them) or plan (avoids triggering the pro rata tax computation) and if you convert right away (so that there are no earnings on which you need to pay taxes). Because any conversion, whether related to Back Door or not, is going to be computed for tax purposes as pro rata to basis. If I put only nondeductible money into a Traditional IRA and do not invest it, so it just sits there with no growth, I can convert it to Roth at any time tax free; backdoor or not, it's just Conversion with nothing to pro rata compute.

"we rolled his IRA's and Roth's to a new firm in August."..."He has no other IRA balances. So no aggregation or basis issues that I can see."

Which is true? If there are no other accounts, and if you confirm that too much was contributed for 2020, you have to remove it from the Roth.

https://www.irs.gov/pub/irs-pdf/i1099r.pdf

And if so, I would confirm if you might still be within the 60-day rollover period, to Remove this from Roth, back to an IRA and then do a new conversion for 2021. Because if you confirm both May 2020 and Dec 2020 deposits are for the tax year 2020, that makes Dec the excess and the rollover makes it a wash event.

I recommend finding someone locally to review all of this with you and with the paperwork that matters.