This paper presents the requirements engineering work conducted in the Go-Lab project, which aims to improve science education by enabling teachers to deploy online labs and scaffolding apps to enrich the traditional classroom-based teaching and learning. We tackled the challenge of developing a Participatory Design approach to address the specific arrangement of the project where the initial user-based requirements engineering process and the technical implementation process were launched at about the same time instead of running the two processes one after the other. To support the PD activities, PDot, an online tool to gather user requirements and feedback, has been developed. In this paper, we present the design of PDot together with preliminary usability and User Experience evaluation results and future development plans. By presenting our challenges and approaches we aim to stimulate discussions about our proposed solution and possible improvements and to inspire other research projects with similar setups.