Unless you for some reason absolutely have to control a portion of the surface, don't bother with a roofed enclosure, every time i've tried to build one in an evil biome, i've had zombie bird and nasty rain troubles. Just dig in immediately, with a 3 wide ramp and an underground trade depot (which you might want to dig out later, after you've delved secure lodgings). Moving everything indoors, and either wall off the enrance or shut it with a bridge or locked doors. Since grazing won't be possible for a while, butcher the pack animals. If you're in a zombifying biome, separate the butcher shop and tannery and refuse pile from the rest of the fortress with traps and lockable doors.
Consider embarking on the edge of a non evil biome, so you have a safe place to put your butchery and refuse storage, as well as an entrance out of the rain. If you make the nonevil biome the center tile of your embark, you will start on it, if you're worried about your dwarves faces necrosing 5 seconds after embark.
Make liberal use of traps, and not just at the entrances. Put them in any chokepoints in the fortress, at entrances to stairwells, around the meeting area, near any potential source of corpses, like butcher shops and hosptials. Make the ones in the hospital cage traps, as dwarves may pass out in there.
Poultry are handy, and not a major risk if they die. If you have a few hens, you don't need to bring more than just the first meal's worth of food.