if i apply for residency whilst i am on the 2nd year of my partner work visa - does that mean i will still get 2 years on a resident visa?
What people often do is to apply for Residence as a partner as soon as they have 12 months' evidence of partnership, even though this is before the end of their first year's partner-sponsored work visa (because they have to have had several weeks' evidence at least in order to get the work visa). Depending on how long evidence they had first, it's JUST possible the Residence might come through and save them having to get a second year's work visa. But anyway, the Residence application will be being processed asap. They get the second year's work visa if necessary. Whenever the Residence visa is put in the passport, it 'takes over' from the work visa. And, as eternalkiwi says, the two years' travel conditions are from the time you become a Resident (on a residence visa in NZ, not resident with a small r, as in living there).
Does it mean that once i've used my 2 years partner work visa, my residence visa would then start afresh - not including the time already on a partner work visa??
You don't always 'use' the time on a visa completely, life not being as tidy and convenient as that! As mentioned above, Residence trumps work visa and takes over, whenever it's granted and put in your passport.