A Philippine national doesn't need a visa to transit Sydney airside for a layover of 8 hours or less, according to Timatic, which is the database airlines use to verify passengers' travel documents.
Visa required, except for Nationals of Philippines transiting through Perth (PER) with a confirmed onward ticket for a flight to a third country within 8 hours. They must stay in the international transit area of the airport and have documents required for the next destination.
- TWOV does not apply when transiting between T1/T2 and T3/T4 at Perth (PER).
Visa required, except for Nationals of Philippines transiting through Cairns (CNS) or Sydney (SYD) with a confirmed onward ticket for a flight to a third country within 8 hours on the same calendar day. They must stay in the international transit area of the airport and have documents required for the next destination.
Visa required, except for Nationals of Philippines transiting through Adelaide (ADL) with a confirmed onward ticket for a flight to a third country within 8 hours on the same calendar day. When transiting on different aircraft, the airline must give advance notice. They must have documents required for the next destination.
Visa required, except for Nationals of Philippines transiting through Gold Coast (OOL) with a confirmed onward ticket for a flight to a third country within 2 hours or arriving and departing on the same aircraft. They must stay in the international transit area of the airport and have documents required for the next destination.
Visa required, except for Nationals of Philippines transiting through Brisbane (BNE), Darwin (DRW) or Melbourne (MEL) with a confirmed onward ticket for a flight to a third country within 8 hours. They must stay in the international transit area of the airport and have documents required for the next destination.
So a single entry visa will be fine for visiting Australia before going to New Zealand, and then no visa is needed for the return transit. But you can still apply for a multiple entry visa; you just might get it anyway.