Originally posted by sarteck:

but I always destroyed the bottom row of stairs after each use. With no ways for the enemies to get in,

another thing that works, if a bit on the cheesy side, is to leave a small 'air gap'. i use floor panels. it should be small enough that you can walk over it w/ or w/out a cart (about the width of the horizontal item stands). it breaks the path finding of mobs and they wont cross over it. works just like a cattle guard.