I had a similar situation a while ago when we renovated the entire yard.* I dug up 500 plants and had to store them over the winter.* I'm in zone 7 in Maryland.* I sunk the pots into the soil up to their rims and mulched to the inner edge of the pots.* I found that I only lost about 10 plants and most of those were the smaller pots as you've described.*
I would suggest you upgrade to one gallon pots in early September if at all possible.* Then sink the pots into the ground up to their rims for the winter.* Mulch the entire bed well, especially after a hard frost.* The idea is to make sure the ground around the pots doesn't freeze and thaw and freeze again.* You'll want to have the soil level at or very close to the top rim of the pots.* Otherwise too much water from melting snow can collect and freeze and thaw and freeze again around the crown of the plants.* In the spring you can remove the mulch and pull the pots.
When weeding, the best way to make sure you are removing a weed and not a valuable plant is to pull on it. If it comes out of the ground easily, it is a valuable plant.