Hi @Vlad
There isn’t a way to tag them via the API unfortunately.
There are a few ways to link payments to invoices however, depending on your situation.
If you are creating purchases via the API, there is an option to create a tagged transaction (for reference). However, there isn’t an option to do this for sales invoices.
We also offer a bulk tagging feature on the bank statement screen itself. There’s more on this here.
However, we can certainly consider a new API method, but generally like to see interest from the community before looking into this further.
I hope that helps