This topic will answer most of your questions/guide you to help you reserve your seats for specific trains (and most other questions you’ve asked before when coming to reservations) :

(Look at Hungarian and Czech Railway pages)

Is this the smartest way to get from Sofia to Prague?

Another question: how long before the train ride do you have to/can you activate the ride? could you activate the ride here e.g. only 21:39?

The only requirement is that you activate it before you board. It is strongly advised not to activate anything in advance: that applies to your pass, travel days (on a flexipass) and inbound/outbound journeys. You can only cancel activation until 23:59 before validity starts. If something happens after that, e.g. you wake up ill, then it will be too late and you will loose travel days, an inbound/outbound etc.

So if your trip hasn't started yet, the best is to cancel activation of your pass and only activate it a few minutes before you take your first train.