A method of configuring a programmable integrated circuit device with a user logic design includes analyzing the user logic design to identify unidirectional logic paths within the user logic design and cyclic logic paths within the user logic design, assigning the cyclic logic paths to logic in a first portion of the programmable integrated circuit device that operates at a first data rate, assigning the unidirectional logic paths to logic in a second portion of the programmable integrated circuit device that operates at a second data rate lower than the first data rate, and pipelining the unidirectional data paths in the second portion of the programmable integrated circuit device to compensate for the lower second data rate. A programmable integrated circuit device adapted to carry out such method may have logic regions operating at different rates, including logic regions with programmably selectable data rates.