MCQ paper Checking should be done in that computer in which main MCQ question paper is stored.
While using data capture section, “different answer sheet” option should be selected below.
While scanning the second bunch of scanned pdf, do not use “layout detection” option, otherwise randomization will occur.
Make sure that whether you are dealing with MCQ Paper-1 or Paper-2, there must have some identification to differentiate whether it is OMR sheets of paper-1 or paper-2. Because there is high chances of mismatch error. For example, you might have scanned OMR sheets of paper-1 and would match those sheets with MCQ question paper-2 then all answers will be wrongly checked. In this type of error, you may found that marks of all students are less by just eye balling over total marks.
Individual OMR sheet should have identification over it whether it belongs to paper-1 or paper-2 for minimizing the above mentioned mismatch error.
for giving title to omr sheet-