Once the software and network have been selected, work can begin on the actual system configuration. Again, vendors can provide extensive help in setting up their respective pieces of the system. The internal portion requires the most attention from the EDI staff assigned to the project.

How an EDI system is designed and developed depends on the amount of custom work an organisation plans to expend. A turnkey EDI system running on a PC requires little development beyond the vendor’s recommendations. A large scale EDI system that integrates EDI with other corporate applications and serves several departments requires a great deal of internal programming and data routing.

For most EDI systems, the greatest development task is integrating EDI systems with existing corporate applications. Data required by trading partners and EDI standards must be "mapped" onto data contained in existing systems. Software must be designed and developed to take the file output of an internal application and move it in to and out of the EDI software. The greatest cost of an EDI system can lie in developing software for integration purposes. Prototyping methodologies, where system prototypes are developed before systems are actually coded, and Computer Aided Software Engineering (CASE) tools help to streamline system development. Integration usually consists of three key activities:

• The data analysis portion of mapping
• Mapping via the EDI software
• Development of any custom interface programs or user exits

Before integrating to a licensed package, the EDI team should ask whether steps 2 and 3 have already been done by the software development firm. This could impact whether they will be able to integrate to your back-office systems without the need for further development costs.