My method is to have specific decks for when I'm first learning something, and more general decks for things I've learned a while ago.
My specific decks are for things I am currently working on. These may be for courses I am taking or textbooks I am reading. Examples are 'control systems', 'thermodynamics', or 'nuclear reactor theory'. Having them separate like this allows me to cram if needed, such as before a test. Also, if I fall behind I can catch up by studying these decks first.
I have more general decks for things I've completed learning. For example, I might move my three above example decks into a more general 'engineering' deck once I've finished those courses. This allows me to keep my number of decks low, and mixes up the cards pretty well.
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I have a system for reading difficult textbooks that I find works well. The basic idea behind my method is that the subject matter is easy once you have the right cached thoughts, so use spaced repetition to cache those thoughts before learning the difficult parts.
For the first reading, have a notebook handy. Make a note of all terminology, definitions, etc.. Don't spend too much time trying to understand it all, and don't do any of the exercises or problems. The purpose of this step is to identify any things that will help you understand the material. For example, if a derivation uses a math identity you don't have memorized, make a note of it.
The second step, which I usually do on the next day, is to take each item I noted in my notebook and put it into my spaced repetition software. This has the added benefit of making me reread just the most important concepts in a chapter. After they are in SRS, I'll do go through my SRS study.
The third step, which I usually do on the third day (after doing my SRS reps for the day), is to read the chapter thoroughly. This is where I'll do the exercises and practice problems.
Steps 1 and 3 take the longest, so if I'm working two textbooks, I'll have them offset on days, with textbook A will be on step 2 when textbook B is on step 1, etc.
This may not be fastest way to read, but I find it works well. It takes me about a month to get through a single textbook, which is why I read multiple texts in parallel-- it also takes about a month for me to read three textbooks. The use of SRS also helps with retention of the material after I've finished the text.