Please help .. Region Confusion !!!

So friends and are were messing around on a flat world that i generated on my server. Than when we had our fun i put the old world back. But some how the worlds combined and now everything we did in the flat world (including a spawning of over 1000 diamond blocks) is still there with my official server spawn !!!!. SO i need to figure out which region files my spawn is.
What I am thinking of doing is getting the exact files where my spawn is than deleting the world and drag in the correct spawn files.
Will this work, And how can I figure out the exact files. The dinnerbone.com website is a little confusing because I don't know how to put in the cords to many chunks at once. Someone please help !!!