Because you are pursuing Biology as an additional subject to qualify for NEET, it is understood that you will have 2 marks sheets and that is totally acceptable. Most States have offline document verification and so it can be easily explained as to why you have 2 marks sheets. What is important is you secure the minimum required aggregate in Physics, Chemistry and Biology. It is 50% for General Category, 45% for PWD and 40% for OBC,SC,ST.