A programmable device may have logic circuitry formed in a top die and memory and specialized processing blocks formed in a bottom die, where the top die is stacked directly on top of the bottom die in a face-to-face configuration. The logic circuitry may include logic sectors, logic array blocks, logic elements, and other types of logic regions. The memory blocks may include large banks of multiport memory for storing data. The specialized processing blocks may include multipliers, adders, and other arithmetic components. The logic circuitry may access the memory and specialized processing blocks via an address encoded scheme. Configured in this way, the maximum operating frequency of the programmable device can be optimized such that critical paths will no longer need to traverse any unused memory and specialized processing blocks.