You can also disable highlighting entirely in the reader settings. Then, you only tap / click the words you are interested in, the rest will be moved to the known pile, either by turning the page or finishing the lesson (depending on the setting).

I don't know of a way for Lingq to treat different case-forms of a word as the "same word". My method is to change blue words into white, word-by-word, until I have covered all the case-forms.

I think you will succeed with your plans for Russian literature, and I think Lingq can be a major part of your plans.

Here is a hint for long novels. Lingq tries to split anything over about 2000 words into more than one Lingq Lesson. A long chapter in a Russian novel will be more than 2000 words. If you hit a long chapter in a long novel, the names of the resulting Lessons can be confusing. For Dostoevsky and other cases where chapters are long, be prepared to do some Lesson renaming, to help you keep track of what is what. Here is an example of a Lesson name that I chose: "Crime and Punishment Overall Lesson 4 (P1 C2 (2)) " This is my name for the second of three lessons that together cover Часть первая, Глава II. In my case, Часть первая, Глава I has two lessons, and Часть первая, Глава II has three lessons. So the second lesson in Часть первая, Глава II is the fourth lesson overall.

You can set the level of lessons it shows you at Intermediate2 (or whatever.)

as for words known, I’m lazy and would just read what I was going to read, and use the feature that marks blue words as known when you page through.  

I think you should just go through the stories and LinQ what you know, don't try to shortcut anything in case your forgot. I think the worst thing would be to overcount what you know

Load the words in from anki as a story, then click through the pages, adding them to your known words. That way you will quickly synchronize the words you know in anki with the words you should know in lingQ.