Apps for offline manga reading Recently my partner has grown very fond of Anime/Manga of all sorts. She has several applications on her iPhone allowing her to view manga. I would like to know what you all believe the best method is, to perform:


Buy Manga sets in an electronic form, such as Naruto Season 1;
Have an application (iPhone and Windows preferably) to allow us to categorise the manga; e.g. By Rating, Type, Language etc. ;
Allow transfer of library between platforms so that we can read on Windows and iPhone


Here is an example:

I buy Naruto, Season 1 in electronic format and download it to PC as *.mobi, *.pdf
I then edit fields such as category, author, rating, etc. 
I then sync with my iPhone using App_X 


Now I understand that there are plenty of online sites where you can read Manga, but I want to be able to own the manga titles and be able to access them offline, on the road etc. 

I had a look for Book Crawler for iOS which seems like a wonderful application for book management in the sense of "what have I read and what did I rate:, but not for what I need. 

Viz seems like my best option to own the Manga. I am not entirely sure if there are any cheaper alternatives on the market. If I buy via their application then it appears that I am locked onto an iPhone to read the manga. Fair enough, she never uses a computer however I'd like to be able to edit it.

I've used applications like Calibre to edit and tag my books before on Android..so I was hoping for some integration with iPhone to PC.
Well there are a couple of resources but this review page [alternate webarchive link because it was down] might interest you pertaining to certain uses. I'll just leave it as an answer here instead of the comments.
The author titles the post :

This is How You Can Read Manga Legally in 2013

While not quite 2013, it has still many relevant links:
First the author mentions E-manga

Where you can read it: It’s a worldwide service.
How you can read it: Bunch of ways: you can download it in 7 formats (PRC, MOBI, EPUB, PDF, CBZ, Apple EPUB, Kobo EPUB), for a bunch of devices, though it depends for some: PC, iPhone, iPad, iPod, Kindle, Kindle Fire, Android, Nook 6”, Nook Color, Kobo 6”, Kobo Tablets, Sony Readers, Linux, Mac, Windows, and Palm OS, Windows Mobile, Motorola Xoom, Abode Digital Editions, Blackberry, Bebook, Aluratek Libre Pro, Cybook Opus, Digital Reader 1000, EZ Reader by Astak, Hanlin, iLiad, iRiver Story.

The author further provides their social media, email and about links in the review page:

Anything Extra: Registration here
Email: customerservice@emanga.com
Social Media: Twitter, Facebook

He also does a mini-review or commentary of that particular site that he lists which I found quite nice:

They have just about every type of manga you want: Shoujo, Shounen, Seinen, Josei, Yaoi, Yuri, Hentai, the works. They are pretty pricey though, ranging from the $9.99 range or higher for a good portion of their titles. As far as I know, most people don’t like to spend that much for physical books; they’ll probably just laugh at seeing the prices here. Otherwise, they’re one of the few publishers that actually allows you to have files for you to keep.

He goes on in this format, mentioning other sites:

MangaReborn
Gen Manga
Viz Media
Weekly Shonen Jump
Netcomics
Kodansha USA
Yen Press
Vertical Inc
Dark Horse
Seven Seas
SuBLime Manga
Rental
Amimaru Manga
J-Comi
Crunchyroll

While the sites are directly linked here, if you need more information other than where to buy electronically scanned manga, like the reviews for each site, support the author by going to the site.