I'd recommend just continuing what you're already doing - going through Core2k-6k & just figuring things out in context. You didn't say where in Core you are, but if it's near 2k I don't think it's worth adding cards. For most native materials, you'll be coming upon too many unknown words. Hyperborea was okay with a base of 3k but for me that's too low. I guess it just depends on your tolerance for the process. =/
When I started Core6k, I would write down unknown words I read (it was a library book) in a notebook (I can't read books in front of a computer), and then later see if they were in Core and unsuspend them. But this was taking lots of time - first copying the words, and then entering them using the mouse-based IME if I didn't know the reading, and then if they weren't Core words, making cards... It also raised questions like
Is this word common enough to be worth learning? and
Is the TTS pronouncing that correctly? I was dreading reading new material, and it also didn't help that I dislike rereading things. Lots of words ended up being Core6k words anyway, so I decided to forget about the unsuspend-words-as-you-see-them process and just get through Core6k.
Currently, I'm a bit past 5k, and I read things whose words I can look up easily: internet news articles, VNs, and Kindle novels. When I see an unknown word I look it up and move on. This way I get exposure to things above my level and don't get dragged down by vocab. When words repeat I often end up remembering them anyway, but these words tend to vary in usefulness, from the more practical (貢献, contribution) to the less practical (暴走族, club of rabble-rousing reckless-driving delinquents). I'm still debating with myself over Core10k, since the audio isn't as great, so maybe I'll start adding my own words again after I get through Core 6k and new words in
Obunsha's N1-N2 vocab series (~7.5k words total).