Dear Sir,
Taxability shall be as follows :
1) Taxable position shall be simple as taxable service shall be both air travel booking and taxi booking
2) For any number of register services under single service tax registration only one return is required to file.
3) For any tour operator in total package service tax need to be charged on gross value only. You have to collect service tax on gross value and take credit of service tax charged by airlines. Alternatively some operator also charge two separate invoices. One reimbursement invoice for air ticket and other service charges invoice and charge service tax on service charge value only. The only concern in that is that you open the charges charged by you per transaction.
4) This option can be workout only when you issue two separate invoices - one for flight and another for rest of tour package. Big tour company follows this system only to be competitive.