I was booking ticket from Viramgam Junction to Madgaon as cornfirm tickets are available, however I will board from Khed which is more than 500 km from Viramgam. Will there be any problem even if I mentioned boarding station Khed while booking?
Yes, it is fairly common to book tickets from a different source station to get confirmed berths. IRCTC allows you to change the boarding station before 24 hours of the scheduled departure of the train. Please read this page for complete details.