Hi Troutboy
I'll try and give you a few pointers on where to start.
Flathead: Flathead will grab anything that moves but if I had to choose one fly it would be the Clouser Minnow. Lefty Deceiver is not a bad second choice. As for colours, yellow/white, pink/white, and green/white are always what I tie on first but as I said before Flathead will grab anything that moves. Keep in mind that on a 6/7wt casting these flies can be hard work, particularly if it is a little breezy so don't go any bigger than 1/0 flies (I usually use size 1 & 2 on my 6wt)
Bream: Bream a temperamental little buggers, but probably the best all round Bream fly would be the estuary BMS(this topic is probably well and truly still open for debate). These come in various forms to fish various depths as well as various colours. I can not really single out a single colour thats consistently performed better than the others but olive and chartreuse are typically the first colours I reach for. As for other flies, Baited Breath's can be great on sand flats and around shallow weed beds, small natural coloured clousers (size 4 & 6) and there are any number of shrimp and crab imitations that can work in the right situation. Also don't be afraid to throw around an olive wooly bugger if you got one, particularly if it has some flashy material in it.
Whiting: I have never specifically targeted whiting on fly but have caught a few here and there generally on sand flats or near weed beds on flies that have a similar appearance to nippers and shrimp (small clousers, Baited Breaths).
Leaders: 15-20 pound for flathead, as light as the situation allows for bream and whiting, I have used 3 pound on the flats for bream and it is always amazing how the big flathead come out to play when you go so light. I usually go for 6-8 pound for bream, with a max of 10 pound in rough country. Fluorocarbon is best..
Hope it helps
Matt