Most banks (at least in the US) allow a data export, usually in Quicken/OFX or CSV format. I download the transactions from my accounts once a week or so and import it into the tool. (PayPal gets charged to my credit card, so it shows up on the credit card import, no need to track PayPal separately)

I currently use YNAB4, and I've assigned categories to Payees, so when it sees a transaction to e.g., my local Pub, it knows to categorize it as Food. For stuff like Amazon or eBay, I need to manually categorize each transaction, but that takes a minute or two.