How do you use Calibre with your iPad?

[Caleb666]

Hi,

I recently bought an iPad 2 64GB, and I'm so satisfied with my purchase (I'm really glad I didn't go with the boneheaded decision of buying any of the 9.7" eInk readers, they're so much worse).

Anyways, one of the reasons for buying it is that I have a large library of PDF, DjVu and CHM textbooks that I keep iin a separate folder called "Textbooks". They're all organized by folders (Analysis, Discrete Math, Probability, etc...) and I'm fine with that.

But I also have a seperate folder in which I keep books that have nothing to do with the University - you know, fiction, nonfiction, history, politics, philosophy, etc...
That library contains mostly PDF files (with the odd DjVu here and there), EPUB and MOBI books, and I'm really having trouble organizing it, I'm not sure whether to a book goes in a Mystery folder, or under Fiction? Is it History, Politics or Philosophy?

Currently, I simply have an SFTP server (the freeware version of WinSSHD - which is wonderful!) on my home computer, and I use GoodReader to sync those folders back to my iPad. Then using GoodReader I simply browse around and use "Open In..." to open non-PDF files in their respective files.

I discovered Calibre, and from what I saw it helps people manage large ebook collections. Here are a few question I have to those that use it:

• What kind of a system do you have? (folders? Calibre?)
• Do you have a situation similar to mine, where you text ebook formats (such as EPUB, MOBI) and PDFs/DjVus?
• Calibre doesn't care how the files are organized in your filesystem, but you do have to have some kind of order... does that mean that you have to organize the books both in folders and in Calibre?
• If you had a folder system such as mine, and you moved to Calibre, how happy are you with the transition?
• How do you access your Calibre collection from your iPad?
• Edit: If not Calibre, then maybe you could recommend another app that will let me intelligently categorize my books in a folder structure.

Thanks!