Ya u can book it through IRCTC...
In the Coch Selection Option put CXL: Where CX stands for desired coach No like C1, C2, C3 etc and L stands for Lower and U stands for Upper....
You will get your desired seat subject to availability....
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more...
I booked that way "C1U" in 02005 KRMI DD and got a seat in C1 Upper Deck... :)