if running both its my personal and non professional (haha) opinion that BeanCount should be before UnderCut so that BeanCount gets you to the general area of the desired price change then Undercut gets you a bit more tweaked around that area... My -personal- opinion is that the wow market works so well and there really is good demand for items and to not use undercut at all and only use beancount to allow for +/- adjustments of the market line and to ignore everyone else who has auctions up completely (for the purpose of posting at least) except when posting that 'ultra rare sword of super life changing decisions', in those cases I don't allow auc to handle my pricing at all and I use what I believe I can get for the item (on those ultra rares it tends to be more than auc's market line as if someone who wants that ultra rare piece sees it and has the funds there just gonna by it as long as its still within reason of that market price)
undercut should go last, because undercut places it at a specific spot relative to other auctions. If a matcher goes after undercut, it would likely wreck that placement, meaning you wouldn't necessarily be undercutting any more.