Setting Up DT Advice

I am setting up DT for the first time. I am using it to store research articles(PDF) and Web Clippings. I want to keep the single database clean so I use another application for random… short term info (I use StickeyBrain since it syncs w/ my PDA and does not have to be launched to “clip” and reference info). Since DT indexes the material how detailed do you suggest the file structure be? I’m not looking for a lot of extra work but want to do enough to “find” what I look for. I use NoteTaker to write and clip my data from DT. Also… what is your recommended back-up strategy? Do you find Adobe Acrobat and a scanner good for text recognition of scanned printed material? A lot of questions I know but seems like there is a lot of experience in this forum.

Thank you.