People often apply for jobs while they are working, the common reasons are for a higher post or an higher pay. In general terms the rule are in the favour of the employee who is applying for a job that has a higher pay than the exisiting one. There is nothing wrong so far, you have applied for the second job while the results of the first we not even out.
While in central government jobs, although it's a ocean, you need to remember that any breach of protocols, service rules etc would be frowned upon. So, please follow the rules and inform the chain of command about your plans via the proper channel and the events so far in writing.
Continue your first job as usual. If you do get an interview about the second job. Apply for leave stating the reason, if the leave is approved or rejected you will have a notification, attend the next interview, if selected, they there would not be any room for any objection to be raised. If you do get selected for the second job, the follow the guidelines to resign and then join the new job. Be cautious about the dates and deadlines.
Please read the guidelines and the regulations related to technical resignations so that you do not forfeit your service till you join the new job. Please check this out in detail (http://documents.doptcirculars.nic.in/D2/D02est/No_28020_1_2010_Estt_C.pdf)
Point No:15 will apply for you.