M.S.
As far as the entire scan to imported items and that work flow, others can help better as I don't use that method. Leslie is the resident Paperport expert, although she is probably too upset with Paperport at the moment to talk about it. Paperport does allow you to convert tiff files to pdf rapidly.
I always marvel at the number of people who use the Brother MFP. I suppose it is because it is a very good MFP for the money. I have always had an issue with its networkability and lack of exporting pdf files to the desktop.
This link:
http://www.aquaforest.com/en/tiff_versus_pdf.aspwill give you a lot of information on tiff vs pdf. It is almost a tossup, but more and more people are using pdf as it has pretty much become the de facto standard for document archival. It is also more secure. Tiff files do not have any intrinsic method of password protection, etc. Tiff files may be better with scanning and with images, but not enough to favor them over pdf. PDF prints better but not enough to favor them over tiff.
While tiff and pdf readers are both ubiquitous and free and most Windows OS have tiff reading capabilities, I would guess more people you would send documents to would have Acrobat. Websites, by far, use PDF more. A lot of sites will open in pdf and when you go to a site with an article, it almost always gives you a choice between HTML and PDF.
In the end, it is a personal choice. I think if you were in your own little office working with images or whatever, using tiff vs pdf would be a choice. But, in communicating with everyone, I think PDF is a solid choice.