QF does not have a MNL-MEL flight. You would need to go via SYD. MNL/MEL fares do allow a stop in SYD so you would actually be better having the entire lot of flights in one ticket.

You will also avoid paying UO tax (Australian goods and services tax) on the domestic.

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QF do not allow combining any Y and J fare together. However, you can combine any J with any F, and any Y with any W on a half return basis. Only those two combinations are permitted.