Um... I... don't actually know how to manually gen worlds yet...
1) Load dwarf fortress.
2) Select "Design a world with advanced parameters"
3) Copy a parameter set that looks vaguely like what you want: how big, and whether it's completely surrounded by water or not.
4) Rename the copy
5) f6
6) Enter the copy. you will now see a long, long list of parameters for world generation. fiddle with them to your heart's content, but know that messing with some in bad ways can cause a lot of rejects when you gen a world. Now, let's talk about the changes you would make to get what you want...
A 5x5, heavily wooded, deep soil, plentiful metal, flux is nice but not required, any number of caverns but they must be more than 50z deep, NO AQUIFERS, biome is any nonevil, and no volcanism. Also, civilizations are a must. My megaproject is the ultimate in anti-siege warfare, and it'd be pointless without Greenskins and Hippies.
To get more forests and swamps, increase rainfall. there's not much difference between the two, really.
To get plentiful metal(s), change mineral scarcity to 100.
To get your 50z, increase "layers above layer 1" to 50
If you want more sky to build in, also set "Layers above ground" to a higher number.
To prevent evil, change the requested number of evil squares in all sizes of subregion to 0.
To prevent volcanoes, set minimum volcanoes to 0 -- a world usually only gens the minimum. If you also want less igneous rock, you can set the max vulcanism to 50 or lower.
Getting flat lands is harder, since you can't drop the max elevation or the generator won't be able to place mountain peaks, which does bad things.
To avoid rejects, make sure that the generator is not looking for volcanic or dry squares.
To have a better chance of getting the right site, gen a bigger world.
To have a better chance of FUN, gen a longer history (more towers/wars)
Or just check the wiki on advanced world generation.