I'm in my Second Year, I'm planning to give the Gate Exam, should I register for this exam in 2020? Also if not, when I'm in my Third year, I won't be having my 5th Sem marksheet how do I apply then?

If you're in the final year of your course, then only you can apply for GATE examination. In case a student is expected to complete the qualifying criteria in 2020 or later, then he/she has to upload their Provisional Certificate Letter (as issued by the Head of the Institute/Dean/Registrar/Head of Department) or a copy of marks card for Section A of AMIE, etc.