I have one deck only. I use light tagging to separate groups, but I think I’ve encountered a similar issue.
The challenge facing you is one libraries and archives have faced for hundreds of years:
How do we organize the large collection information so that someone can find what they want as efficiently and effectively as possible?
As our mental understandings of the knowledge grows, we’ll find more and more connections between the information stored, right? … which means more categories to search by, more concepts to group by, more keywords to query by…
So far, to solve this for myself:
I’ve binge read (with copious notes taken) Intro to Indexing and Abstracting (Cleveland), Organization of Information (Arlene G Taylor), Douglas Hoff’s systematic analysis on modern mnemonic systems (this guy
@thinkaboutthebible , Hi Doug!
).
Now I’m binge reading Giordano Bruno’s Song of Circe and On the Composition of Images (translated by Scott Gosnell).
Bruno, as far as I can tell, actually had a complete system (or close to it), or what I refer to as a Global Mnemonic System (because I’ve memorized a lot of programming documentation, so a global scope reference is in order for me).
Tips from the folks who design library systems (called Information Architects):
- Determine what all data you have to organize
- Determine what your system’s users (just you) would find most helpful and are most likely to want to find and how they’re most likely to intuitively search for it
and the third tip is a paraphrase of my own analysis up to this point:
- Determine what sorts of Indexing would help you most in finding what you need, then find ways to memorize the indexing systems you develop.
Hope something in this post was helpful or at least got you to say “No way on Earth am i doing that.”
There’s no perfect system.
Ask an “information architect”.
There is only: “What is an intuitive and helpful system based on what my users will seek.”
And in this case, according to the information sciences, you are your user. 
Regards,
Beau
p.s. I’m open-minded to disagreement! Please feel free to disagree and explain why!