1. A computer-implemented method for configuring a target processing entity having a processor, a memory coupled to the processor and a programmable logic device coupled to the processor, to implement a graphical program representing a procedure, the method comprising: creating the graphical program at a host computer system that is different from the target processing entity, the graphical program having a plurality of interconnected blocks defining a procedure; specifying a first portion of the graphical program for execution by the processor of the target processing entity; specifying a second portion of the graphical program for execution by the programmable logic device of the target processing entity, at least one block of the second portion of the graphical program connected to at least one block of the first portion of the graphical program; creating a single build file based on the first and second portions of the graphical program, the build file having an executable code section to implement the first portion of the graphical program, a communication interface section to implement the connection between the at least one block of the first portion with the at least one block of the second portion, and a configuration section to implement the second portion of the graphical program; downloading the single build file from the host computer to the target processing entity; executing the single build file by the processor of the target processing entity, the executing including: storing the executable code section for execution by the processor in the memory of the target processing entity; establishing a communication interface between the processor and the programmable logic device based on the communication interface section; and configuring the programmable logic device with the configuration section; and implementing the graphical program at the target processing entity based on the processing.