As the trading period for the RE’s has now been closed you will not be able to see these shares in your holdings, though they will remain in your Demat account until issue closes, after that these RE’s will be extinguished.
You will not have to apply for rights shares, the process has been explained here.
How to apply for Deepak Fertilizers rights issue?
Once you either receive the RE’s from the company or purchase it from the market, you can apply for the rights shares using Netbanking ASBA, you can check the process in this post . You can verify your entitlement on the website of the Registrar & Transfer Agent . The website will not be completely live until the issue opens.
You will need to enter your demat account’s Beneficiary Owner ID which is a 16-digit number while applying either on the RTA’s website or through Netbanking ASBA.
If you do not apply for rights shares, you will lose the entire amount you have paid to purchase the RE’s.