Introduction
The Zettelkasten method usually implies two kinds of note linking: note sequences and cross-references (links in Obsidian). The problem or characteristic with simple (yet sophisticated) text-based and link-based programs like Obsidian is that they ignore the note sequence principle in order to maintain simplicity and clarity and to avoid too much metadata. You can argue about the question whether a note sequence principle should be omitted because it certainly lacks dynamics and implements a predefined order that actually is yet to be developed in the process. I have come a way from ZKN3 (with note sequence principle) and have decided to exclusively work with cross-references (as Obsidian does). But that depends on your workflow (how ›strong‹ is your systematic/order supposed to be?) and your specific use case.
With that said, the following is my personal workflow.
regarding citation
I agree with @atiz, the literature can simply be collected in a bibliographic management software (I use JabRef although not using LaTeX or BibKeys). There I have a fix and distinct short citation (stored in a custom field) that I use in Obsidian (and other documents like excerpts) and that distinctly points toward the literature.
regarding index
I do the indexing (by this, I guess, you are actually referring to the process of orienting yourself, of keeping an overview and of navigating to certain notes inside your Zettelkasten) in two ways that serve different purposes:
- Tags: All notes (in contrast to Luhmann’s approach) get one or multiple tags that place the note in specific contents in which I want to find/rediscover the note later. When in general searching in a specific thematic field I search for the favoured tag (simply click in the tag pane) and look at the results. My tags are very detailed and deeply nested (at least 4 levels, up to 8 or so). The advantage in Obsidian is that the search for a superordinated tag implies the subordinated tag levels. So you always search for a tag and all subordinated tags. This search query can also be applied to the graph view which does an excellent job in giving you orientation (although there are a few feature requests for the graph view pending). There is also a local graph view that shows only the actual note with its links.
- Maps of Content (MOCs): For a more systematic (and ›predefined‹) search I use »Maps of Content« (MOCs), i.e. notes (notes on a meta level) that contain nested lists, each is a link to a specific note. Here I exclusively place specific thematic focal points (= key aspects of a thematic field). For example there is a MOC for Marx’s Critique of Political Economy where I collect the key aspects of his economic-philosophical thinking (e.g. writings, methodological fundamentals, thematic clusters spanning over different writings). These MOCs require and imply a certain level and quality of development and differentiation of the thematic field. But if you already know that a specific field will be complex and differentiated and know enough of the upcoming thematic aspects and notes, you can create such a MOC from the start. The MOC serves (analogously to Luhmann’s approach, but in a more systematic way, you could say) as a note sequence but the difference is that not every step of certain sequence or argumentation is represented here, rather only the most important steps that serve as points of entry into the note net.
Hopefully this workflow serves as a possible answer for your question.