This is still a great place to start;
http://dwarffortresswiki.org/index.php/v0.31:Advanced_world_generationYou can get rid of aquifers by modding them out in the raws, so that's a yes too.
You can get rid of vampires and werebeasts in the advanced settings by putting 0 in their 'secret' categories.
There has not been much breakthroughs concerning towers yet but it seems that genning a world for atleast a 100 years guarantees atleast one. Get legend viewer and scan your world to find them much faster.
Caverns layers are described in the advanced world gen wiki but; yes and it's really easy. I'd personally recommend you to get some space between the two caverns though; the beasties in there get worse each level so some breathing space between the two gives you time to get used to them.
The temperature thing; I personally reckon you should work with the
http://dwarffortresswiki.org/index.php/v0.31:Advanced_world_generation#Terrain_Mesh_Sizes_and_Weights and get temperature variance either really low[so that you would get two ''zones''] or really high [patchwork world].
Watch out with the preset ''minimum'' demands, better change those to prevent endless rejects.
Oh and, best way to get alot of evil seems to use the minimum evil and boost it up really hard; don't get too much though as that will limit civilisations. Towers also do not seem to spawn in evil, which is handy as this means you can get undead fun in an otherwise peaceful area.