Assuming you're already inside, safe and sound:
a) Eventually, you'll want bridges to block access to your depot, and not just doors. Doors can fall to kobolds, building destroyers, ghosts....
b) Multiple pathways, so that a single zombie in the staircase doesn't stop everything.
c) Hatch covers and doors where convenient, again, to stop LOS problems.
d) Nothing wrong with interior traps. Although plenty of people say to avoid slicers, I think slicers are fine, as there are only a certain number of animate bits that a slicer can make, and you're going to end up with those bits anyways. Cage traps are good too. Keep in mind that so long as you stay walled off, your only real problems (dwarf zombies) are going to be unaffected by your traps (isresident flag checked).
e) Slabs, not coffins.
f) Some form of refuse/graveyard disposal. I would recommend atom-smashing, although magma or just a deep, inaccessible pit will work nicely. The problem, of course, is that this requires oversight. It can be automated if you feel like messing with mechanics, though (I can give you a specific example of how if you want).
g) Underground tree farm. Start it early, and you'll have the fuel you need.
h) You can safely transfer water by pumping it through a grate. Critters can't destroy grates above them. (Again, I can give you a specific example of how to deal with your water problem, if you want.)