In case you have multiple salaries, you can upload different Form 16 one by one, or manually add the data when preparing your ITR.
You may have multiple Form 16 if you changed your jobs during the financial year. In this case, you are required to report all salaries you received during the financial year in the ITR.
From FY 2018-19 onwards, your present employer is required to report the total salary from other employers during the financial year in Form 16 Part B issued by them. However, this Form 16 Part B will only include a total amount and not the detailed breakup of allowances which is required while preparing the ITR.