Unified way to manage annotations and bookmarks in Android and PC
Two options:


backup Mantano's database (or the whole mantano folder)
use Adobe Digital Editions to extract the annotations


The first option will keep you locked in Mantano. The second in ADE, which more applications use it, but it's not as pervasive as one would like. The main problem with .epub is that annotations aren't part of the standard, thus every application that supports it has to implement annotations in their own way, which usually means storing them out of the file.

For PDFs, I use Repligo, which stores the annotations inside the PDF. But many others like ezPDF accomplish this.