We track "everything" in Quicken. We've been using it for so many years, so we have easily two decades of data data to go back on for data mining and comparisons. We use "tap to pay" or "contactless" (android pay) when ever possible to cut down on paper receipts that need to be scanned before destruction, but otherwise we almost never use cash to make it easier to track everything, and we always scan/pdf save each transaction for cross referencing.
I think a new more and online system for users is something like mint, to do this type of tracking and reporting of budget, spend, and actuals. I don't keep our records online so we've kept the old system in place.
As for your original question, about tracking pre-paid stuff, we just separate out the expense in the ledger when necessary to show the cost of an item that was prepaid or covered multiple months, like our 6 month rental contract. You can make a place holder item for the original transaction, then another place holder for the month where the money should be applied/denoted, calculated.
Once the data is recorded, it's super simple to check budgets, estimates and run reports. I'd be interested in hearing if anyone else is using such a system.