Slyder
I don't think there's much you can do to optimize the throughput with the DNS-323 - it is limited by the processing power and memory available in the device.
This is a low cost device, and that is evident in it's performance - having said that, it appears to be, based on SmallNetBuilder reviews, a better performer than many products in the same price bracket.
From my point of view, trying to wring the last megabyte/second out of it is pointless - you can test all you want, and by the way, large file sizes will give you higher numbers - but in a real world situation, where you have no control over file sizes, the throughput is likely to be disappointingly low.
I've seen numbers in to the low 30's in my tests, but in my real world usage with the same hardware, throughput averages at <1MB/sec. It does what I want (backup my server) and I'm happy with it.