Easy ones: If the SIPP is huge and the ISA tiny, pay from the SIPP and ISA (unless you need to reduce your income by maxing out SIPP contributions). If the ISA is huge and the SIPP tiny and you are already paying much tax on dividends/capital gains in a General Investment Account, pay from external bank.
The tax free space in an ISA is valuable, but it only really counts when you are exposed to paying tax on other S&S (which could be far in the future, giving you plenty of time to Bed and ISA) or when it forces you to keep records for tax.
If you get a chance to pay all the fees from the SIPP this is ideal - but I don't think it is possible (or perhaps legal).
Most people with both should pay from the SIPP and ISA.