Restart the DNS server. The server will now read the BIND boot file for its configuration information and here's the nice part update its configuration information in the Registry to match what it read from the boot file.
If you want to the server to use the boot file permanently, you're finished now. You can even add or delete zones using the DNS console; the server will update the boot file. That's a nice improvement over Windows NT, which silently converted back to loading startup data from the Registry if you made any changes with its DNS Manager administration tool.