When you file your late filings through Taxumo, Taxumo will automatically compute the BIR imposed penalties for you. You can, of course, pay this along with your tax payment to Taxumo.
Tax penalties are composed of:
Surcharge: 25% of the tax due is added as a surcharge
Interest: A 12% per annum interest fee is added on the tax payment
Compromise: Depending on how much your tax due is, you will pay a set amount. For zero filings, a P1000 compromise fee is imposed.
All of this is paid one time when you file + pay through Taxumo so it's a one-time convenient payment.