I cut cpvc in half and use those as rails to hold up net pots. I then used black/white poly white side up and cut holes in that and laid that over the top and then put netpots resting on the rails.
I ended up needing a supporting piece in the middle and I never did end up using it as growing that # made me nervous(was for a sog). But I thought it was cheap alternative to those pricey covers and looked tight all plugged up with pots.. But since you bought the cover already id say hole saws. You dont need a big pot since it sounds like you're suspending them, the roots will just grow into the flood table. You could get away with a 4 inch netcup. 4 inch hole saw should be easy to find.