A programming method efficiently programs programmable logic devices of the type having specialized functional blocks. Those blocks may include multipliers and other arithmetic function elements, or may be various types of memory blocks. In order to efficiently program devices having such specialized functional blocks, without using a larger device than necessary, and without failing to fit a user design to a device, if the programming method finds that that there are more functions to be performed in specialized functional blocks than there are specialized functional blocks available, the programming method attempts to map some of the specialized functions to generic programmable logic elements (or other resources), assuming there are sufficient programmable logic elements (or other resources) that otherwise would remain unused in the user design.