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in VTrain, "reminding" you of due reviews is done unobtrusively by way of leds that light up on the Cardfile that is currently open. No pop-ups.
This means that yes, you would need three different Cardfiles to learn your three subjects separately. In fact, that is most college-level users do. This makes sense especially when learning for an exam - those who are sure they will never ever procratinate can as well use a single Cardfile for all subjects.
We believe that opening each of the cardfiles once every day is not too much too ask. After all, it's as easy as browsing a paper calendar: just Press Ctrl+Q, choose the cardfile you wish to open, and press Open.
Feel free to contact us with any other questions you might have.