I am travelling to Switzerland for the first time.
I have booked my train ticket from Basel - > Prague through Bahn.com
I have got the reservation done but I am confused about how, where and when will the seats be allotted to me for journey.
All replies would be greatly appreciated 
Basel to Prague
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Bahn.de is the germann rail web st e- not sure how you booked a ticket from Switzerland to Czech through a German train site. Are you sure that's what you have? Or just a ticket for part of the route through Germany?
And depending on the train there may be no seat allotted. Depends on what type of train it is and your class of travel. It may be festival seating. Typically If you want a specific seat reservation that is an additional cost.
In looking at the Swiss train schedule, sbb.ch, it looks like you have 2 changes of trains, ending with a bus trip.
http://fahrplan.sbb.ch/bin/query.exe/en?OK#focus
Is this what you think you have.
The good news is that the bus between Nurenburg and Prague is modern and nonstop. The train tracks are very old, so the bus is much quicker.
Basel also has a German (DB) train station: Basel Bad(ischer) B(ahnho)f. The ticket is probably booked from there. On the other hand, it's totally possible to book a trip from Switzerland through Germany to Prague on www.bahn.de
Also, there is a night train from Zürich via Basel, Frankfurt, Dresden to Prague. Maybe the OP booked this one.