I am using MCC Pilotlog too and it does auto-recognize flight numbers.
Once you have done the same flight before, or even another flight with a similar flight number that meets a specified format. So you don't need to upload any list, it just searches the database for the same or similar flights with the same carrier.
e.g. our morning flight from LAX to CLD is 6205, the same flight in the afternoon is 6209, then the software will recognize 6205 when you enter 6209
It does also calculate sector pay according to the rules to be entered.
Not sure if these features are available from the free version, I have the professional edition running (with Google Earth)