Under bottomscanner under the evaluator the appraiser settings under the advanced settings i see a "use market matching vales from appraiser" if i mark this will it use my adjusted stddev values since beancount is adjusting them?
yes, if you don't mark it it will just use stddev without the adjusted value (but it does slow a scan down a tinsy bit to have it enabled -- but I believe it is well worth using the adjusted price... )