Currently I have a couple of virtual environments. But they all share one .prodigy containing prodigy.db and prodigy.json. Can I make one for each virtual env?
Yes, Prodigy also supports reading from a prodigy.json in the current working directory, which overrides the global settings. So you can use the global prodigy.json in your user home directory to specify general settings (like the theme to use etc.) and have a separate prodigy.json that defines project-specific settings and overrides. In that prodigy.json, you can aso point to different database files. See here for details: https://prodi.gy/docs/api-database#setup-sqlite