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?

[DoninGA]

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

[Opus 17]

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.