Yes Kartik those resources are supposed to be used in a Dark set. But because of the shop being uncooperative, the upgrades are delayed until I get the item that I need. Including buying of limited items stuff. They will be used, all of them. I'm just waiting for that item. Last night I only got a dark armor in the shop and it's such a waste of souls.
About the upgrades.. I haven't reached the thousands yet cause of limited stones in inventory. Also time is inadequate for hunting. I play mostly on weekends and holidays for longer periods of time. How about you, have you reached the 1,000 upgrade yet?