At the moment, it’s not possible to display multiple imported GPX tracks on Mapy.cz and plan a new route over them. This feature has been requested repeatedly in the past, including on the previous version of the forum. The team at Mapy.cz is aware of the demand and it’s planned for the future. The goal is to allow keeping tracks - and also waypoints - visible while planning, organized by folders where the GPX files are stored. However, there is currently no timeline for when this will be available.
For now, there's a workaround using the external site gpxmapy.cz. It’s a GPX editor primarily intended for editing, merging, extending, and fixing GPX files. Since such functions require route planning, the site includes planner. And this planner allows exactly what you're asking for - the imported tracks remain visible in the background while you plan a new one. However, compared to Mapy.com, the planning options are more limited - for example, it doesn’t include all routing modes or POIs.
You can load your GPX files there, plan a new base route, and then export either the GPX file or directly transfer the plan into Mapy.com. This is likely what you need - a new Mapy.com tab will open with the same planned route, which you can then save to your account and fine-tune further. You’ll then be able to navigate based on that.
Please note that gpxmapy.cz doesn’t have a mobile app and is only available for desktop. It is available in English. Uses the same map base (via API from Mapy.com) Think of it as a toolkit designed to work alongside Mapy.com - for example, you can even convert a track directly into a route plan see here
