Some of the boxes on my W-2 form weren’t filled in, so I can’t fill it into the online form, does it matter if I leave those blank?

If your W-2 has boxes with no entries then do not enter anything in the TurboTax W-2 for the same boxes.

If you have an error message in the program, let us know.  But almost all the time, you enter what is there and leave blank what is blank.   Not all W-2 possibilities apply to all workers.