Ask HN: How to create a Mac library of electronic magazines – with bookmarks?

For my Mac, I would love to a) have a library for magazines in PDF and possibly other formats also, and b) create bookmarks in this archive AND have a system/index for these bookmarks.

I've looked at Calibre, iBooks and Zinio, but I'm none the wiser.

Calibre lets you add documents as PDF and edit metadata, but there are two problems.

Firstly I found no way to create bookmarks that you can view on a SYSTEM basis, meaning that I can look at a list of ALL bookmarks for ALL files in the database and select e.g. "Interview: William Orbit" or "Cooking: Tomato Soup" etc.

Secondly, if you open up large PDFs it takes forever to open them in the internal Calibre browser, while with Apple Preview it takes just a second.

Any other ideas? Thanks!