I have caught Flounder on rod and reel using a number of methods, First is just spinning using 7-15g trout spinners just dragging them along the bottom, Only really works if there is high concentration of flounders. Second is using 3 inch Gulp threaded onto a longshank hook with a sinker about 1m above and let a drift down in the current Can also use a Jighead too Just make sure its being dragged across the bottom, Third is Bait which is probably the best option unless flounder concentrations are very high. Normally make my trace out of 10lb mono using a size 10 Trout hook with a sinker above and below the bait.sea worms are the best bait but normal worms are fine also, if you cant get any worms Small Shrimps from the Supermarket work ok too.
Yabbies/ghost shrimps you get from in the sand at beach along with sea worms are too baits, try a sabiki rig with sinker at each end of trace, have caught them on the coast on mussels , speared heaps around kaiapoi and also caught loads in a set net
Both species eat a most types of bait, but Pilchard and Squid are safe options and are readily available. Fresh Kahawai fillet is a excellent Snapper bait. Fish can be fussy at times, and would only take a certain type of baits so Its a good idea to bring and use more then one type.