what perry said, it will be contaminated.......don't treat if you will use any boxes left on for the bees that honey will be harvested from in the future...........
i would suggest that you use apiguard rather than the api life var........
if you choose to treat, take the boxes you want to leave for their reserves and your future honey boxes off. treat, and once treatment is complete, you can place them back on.
it it's your first year, and these are first year bees/queens, mite levels may not be very high, so you may not have to treat. it just depends on where your bees came from and if there are other hives around you. but that said, be vigilant. you need them to be strong going into winter months.
good luck!