I understand that if there isn’t a sufficient balance in a Pot to pay Direct Debits, for example, from the Pot, then it will be paid from the Main Balance.
But what happens in the opposite case where, for example, all of my money is in Pots and there is a Direct Debit due from the Main Balance?
You get a notification in advance that there isn’t enough money for your direct debit, so you then have plenty of time to move some money from a pot.
If a direct debit fails, you also have the option to retry, so you’re double covered.
If you don’t have enough money in your main balance, you will either have your Direct Debit decline (but you can retry once), or it will go into your overdraft (if you have one). If you do go into overdraft then you will be liable for any overdraft fees, even if you have money in pots.
Direct Debit payments come from your main account, Monzo just move the money from your chosen pot into your main account if you’ve told Monzo to do that for that specific direct debit. They won’t take from a pot unless you have specifically told them to, as the idea is that you have allocated money in that pot for that payment.
(Hopefully that makes sense)
Monzo will notify you; and give you until 2:30 to make funds available, or by memory you can add funds and tap pay now or similar on the direct debit transaction screen.
Hi @VoTB & welcome 
For clarification, the payments are always (and only) paid from the main account. The difference with a designated Bills pot payment is that Monzo automagically transfers the exact amount to cover the planned payment from the pot to the main account microseconds before the planned payment is taken from the main account.