Seki stones should be left as alive (i.e., not marked as dead which fades them out). For Japanese rules, any eyes held by stones in seki should also be marked as non-points (which the site shows as small blue squares) by clicking on those points.
The Japanese rules have all sorts of complications, and anti-seki is certainly one of them. However, stones that are technically dead under anti-seki are not removed from the board for scoring purposes, so for the sake of scoring anti-sekis properly on this site, those dead stones in anti-seki are also left as alive. Or so, I think, but there are always weird edge cases in the Japanese rules, so maybe someone can find a convoluted example where that’s not even correct.
I’ve written about anti-seki in another thread over several posts starting here: