For some questions, my parents have the boxes blank. Would I put zero?
For example, when asked about income taxes (my parents file 1040) lines 56 minus 46, both are blank.
Line 56 of the 1040 should have a number in it, even if it’s zero. It should not be left blank. If line 56 of the 1040 is indeed 0, and there is nothing entered on line 46, then the FAFSA question that asks about line 56 minus line 46 would be answered with a zero.