but we have to use the transport counters (trucks) for Rail cap?
No, as long as you follow the entraint and detrain rules (13.3c) you don't need any transport counters for rail-transport. However you cannot combine rail and transport units in the same phase (no leapfrogging).
how can I put the rest of the trasnport counters in play?
Those extra counters could be used as "change". In other words you could combine two 2T counters into one 1(SP) counter.