Not sure why you have created a dkp system for each raid instance, but I can answer your question a little bit and give you some tips.
You can select items by the zone it's in with the options at the top. Then what I do, because it constantly refresh's and changes the defaults back if you edit off that page, is I right click and open target in new tab and then edit that value.
This is still a "one item at a time" approach, which is fine if you have differing values.
95% of the items in a given zone have the same base value in our system, so what I'd like is a way to change ALL the values of ALL the items in a given zone. At the top of the "Quick Edit Items" an input box that if you put a value in there and then submitted made it that value for the entire column would be ideal.
As for why I have mulitple DKP systems - there are a number of reasons.
1: DKP going into the system is different between 25 man and 10 man raids if you use static earning (which we do) and can also vary depending on how many bosses are in a given system. I need to balance this with dkp out, so I need varying item costs based on instance.
2: I want to avoid people collecting DKP in an easy/farmable instance and hoping to hoard the loot in new content by spending it there. I believe this doesn't encourage people to show up for progression-based raids.
3: I simply find it easier to track raid attendance/items recieved/etc based on instance (personal preference)
=)