Tax return still in process… but I want to make payments!!!

We filed an extension to send our personal/business taxes by September 15th. My accountant finally sent them on October 12th and both the state and federal returns are both "processing."

2024 was a really tough year mentally and I stupidly paid no quarterly taxes (small business owner) 🙃 Anyway, we owe about $2k to the state and $5k to federal.

When our accountant filed, we didn't pay right away. I'd like to make payments to the IRS but I'm afraid that what if I make them and they don't somehow go to the right place? I am planing to apply for a payment plan, but I can't do that because my balance is currently $0 (since our return is processing).

If I make payments online and select Balance Due, Income Tax – Form 1040, 2024, should I have any worry that when my return is FINALLY processed that the payments won't be applied to my return?

Thanks.