LongLats, if you enter YSSY as both departure and destination with YBBN as a via point, you can then just enter the total flight time as per your second example. However by doing so you lose some functionality.
If you want to search how many times you've been to YBBN, it won't recognise the via point as a landing point. Also the program won't be able to calculate night flight, which it can do if you enter off blocks/on blocks per sector.
All of my LTP entries up to a year ago were in that format then a pilot I was flying with showed me the search feature, and I now log each sector by block time. On a multi sector day, enter the sign on time on the first sector, then sign off on the last, and it'll calculate total duty for the calendar day.