For example - I know that 작 means “small”. But I have never come across the word 작 standing alone.
Instead it’s 작나요; 작아요; 작다고요; 작냐고 and many other varients.
I’m working on learning grammar but so far, I’ve only learned and understand 은/는 and 이/가.
I have not even started conjugating verbs yet. But will I be slowing my progress on Lingq by marking 작[followed by whatever] as “known”?
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You mean if you don’t know the grammar? I tend to mark them known unless someone put a good grammar explanation into LingQ which is really rare.
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I think it’s entirely up to you. Keep in mind that the system is for you to use in whatever way you’d like. It shouldn’t effect your progress at all. Whether you know the word and form or not doesn’t depend on whether you’ve marked it as known or not. I don’t worry much about marking specific grammar when I’m reading and using LingQ for Korean. It’s too much and I find that I get more information about the grammar when I simply know all the words in the sentence. I’d also say that it’s going to take a very long time until you process the more specific Korean endings and connective endings with any kind of automaticity. Certainly don’t expect to speak using all of them until you’re at an incredibly advanced level. The ones you have listed in your post you’ll get down much earlier (based on my experience), but others will still not click for a while (many still don’t for me yet). Your known words in Korean will jump quite high, but that’s mostly just because of how the LingQ system counts words. I would say don’t worry as much about marking all the forms in each LingQ but mark every form you encounter of an unknown word, even if you see it 10+ times in different forms in the same reading. It’s a bit tedious, but since the goal is to understand the passage and later passage better with the hints, I think it’s the best strategy. It still allows you to make use of the hint later on as well which is the main function of making LingQs. If there is a specific grammar pattern that’s been particularly elusive for me, I’ll often highlight the phrase/word and only put in the grammar explanation. I’m still not convinced that is a worthwhile use of my time though 
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Why wouldn’t you mark something known if you know it?
No, you should not. The whole point of the LingQ system of marking individual words is to learn how grammar alters a word. In many languages, including Korean, there is a big difference between the word for “run” and he word for “I would have ran.” You may know “run” but if you don’t know “would have ran” then you should not mark it as known.
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