A programming tool for programmable logic devices (PLDs), such as field programmable gate arrays (FPGAs), supports the display of hidden-switch connections, in addition to the display of conventional placed-switch, switch-box, and pseudo-arc connections. A hidden-switch connection between two functional elements in the PLD is represented in graphical displays generated by the programming tool as a curve (e.g., a diagonal straight line) from a jumper wire on the first functional element to another jumper wire on the second functional element, where a jumper wire is represented in the graphical display as a wire connected at one end to an pin of the corresponding functional element and unconnected at the other end. A programming tool that supports hidden-switch connections can be used to program FPGAs and other PLDs having architectures that were not previously supported by conventional programming tools that do not support hidden-switch connections.