Oooh, I am going to jump on this and hopefully get some more attention for you. First things first, a lot of the folks here will advise you to search the forums for an answer to your question, since many of these issues are fairly common, and there is some great advice here.
It is my opinion that the system drive should not be as large as the other drives, since it's really not a good idea to put your data on the system drive, anyway. Again, that's opinion. Mine is based on the fact that the system drive is going to get a lot more work than the others, and you can even witness this for yourself, if you decide to install any of the good drive managment add-ins.
The only reason to make your system drive substantially larger is to serve as a fail-safe in case one of your other drives kick the bucket and you have folder duplication set.
As far as best practices go, I was too excited to receive my EX470, and so did not run it in a test environment first, with the option of upgrading/replacing the system drive with something bigger/quieter/more efficient. As I am sure others here would advise you, the earlier you replace your drive, the better - before data is written to the system drive. Hope it's not too late...
EX470, 2 GB RAM, 2x500GB, pooled; homebuilt WHS 160GB+2TB pooled; Dell Inspiron 1545, 4GB RAM, Win7 Home Prem x64; Macbook 13"; Homebuilt AMD Phenom BlackX4 8GB RAM, Windows 7 Enterprise x64, 250 GB system, 1 TB RAID 0 data