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"Unfortunately, PDF Fusion
was not designed to fill out PDF forms. It
sounds like you may have used the free text tool in PDF. On most
PDFs this works well, but in the case of Fillable PDFs the form
fields tend to be displayed in front of any other text,
including the text you added.
For filling out PDF forms, my
recommendation is to use Adobe Acrobat or Adobe Acrobat Reader.
Both are very capable at filling out PDF forms, and Adobe
Acrobat Reader is a free product from Adobe.
PDF Fusion is a great option for updating
other PDFs, merging multiple PDFs into one, or removing pages
from a PDF.