The Education through Virtual Experience (EVE) research group based at the National University of Ireland Maynooth have successfully developed an online Virtual Learning Environment (VLE) for Astronomy as part of the Virtual Telescopes in Education (VTIE) project. The VTIE VLE has been developed to provide online software support for the engagement of schoolchildren and their teachers in a scientific process. The development of an online VLE to support a scientific process has brought about complex interactions from the user perspective. This has lead to complex integration and communication challenges from the software implementation perspective. This paper contains a high level user-centered summary of the integration and communication challenges that have arisen during the VLE development and summarizes the mechanisms used to meet these challenges.