I breastfeed 3 kids for at least 1 year each. My first was in day care part time so I had to pump and store and make bottles for daycare. This is my advice.
It changes depending on what you are going to do with the stored milk. In the beginning when the baby is small and not drinking much, I used the bags and only put about 2 ounces in each bag so you don't waste much. Easy for husband to defrost and feed. Release most of the air before closing the bag and store upright(difficult to do) in freezer away from everything. Not so much from contamination, but because other boxes can tear holes in the bag and you will never be able to defrost the milk without it leaking out. The bags are fragile and rough handling could cause holes or split seams. I didn't have any problems with the bags and I used several different brands, but my friend always had leaks when she defrosted them. Also, the bags are easy to defrost under running water. The bottles take more time.
When I was engorged and pumped to relieve the pressure I would use the bottles and fill them to the top before storing in the freezer and save them for when the baby was a little older and drank more.
If you are storing breastmilk for later use like to take to daycare then I would use the plastic bottles. Or if you do use bags(they do hold more), you should defrost the milk and make bottles to take to daycare. Don't ask daycare to defrost bags and make bottles, they are messy and I fear they will waste more breastmilk than you will ever know.
When I was in the hospital, they gave me dozens of bottles with lids, disposable nipples and labels. The bottles fit on the breastpump breast funnel cups so you don't have worry about transferring the breastmilk. The bottles that come with the breastpump(bottles with yellow lids) are good too, but expensive and small. The bottles from the hospital are small too, but they are free. I didn't use the bottles to feed my baby as I didn't have nearly enough nipples; I just used the bottles for storing and freezing.
Another thing, I never used the special bottles that are made to hold the bags. I just poured the milk from the bags into regular bottles.
Congratulations and Good luck.