Putting up RAID for desktop use , need advice!

Think about your needs, you want:
1) performance for your system disk / files that you want to be fast
2) storage space / protection for data you do not want to loose

So pick a solution that fits both needs. A Velociraptor or SSD for your system drive (performance) and two 500GB drives for your important data; either in RAID-1 or without RAID and let one 500GB drive be a copy of the other; this offers more protection than RAID1 and you don't need any RAID-drivers, which can be a pain.

Don't make the mistake of creating a RAID0 and not having any protection for your data. Performance is nice, but performance doesn't do you any good if you lost all your important files.

Sure that would work. Because the RAID0 is not the volume you boot from (you boot from the velociraptor) you do not need any special RAID-drivers during setup. You have both speed and a backup.

2x 500GB in RAID0 would be 1000GB yes, or 932GiB. The stripesize is often 64KiB or 128KiB; it depends on the driver implementation which one works best. Normally i would advise a 128KiB stripesize.

If you use Windows XP, you need to take special care on striping RAID systems to avoid a misalignment issue. This causes lower performance than should be, but can be corrected by setting up the partition table the right way. Windows Vista and Windows 7 are known to do this, but for Windows XP you need to do this manually. Since its not your boot drive, this can be done with third party utilities. You could also use Vista/Win7 DVD temporarily to create a partition, then switch back to XP and use it. For this to work you need to boot from the Vista/Win7 DVD and install raid drivers via USB pendrive. After the partition is created, wait a few seconds then hit reset and take out the DVD. Now you can continue to boot XP again and it should find your new partition on the RAID-array.

If you let XP make the partition, your RAID may be slower, especially for random I/O.

Cluster size is a filesystem setting, its not directly related to your RAID; although if you're only working with large files you may enlarge this value.

You said your controller is JMicron, know that these RAID drivers give lower performance. You may therefore also consider using software RAID instead on the JMicron controller, or use your chipset-powered SATA ports instead, unless you have ICH9/ICH10 without RAID. If your chipset does feature SATA RAID you can use this for the RAID and JMicron for your DVD/single disks.

You have ICH9R southbridge, the R means you got RAID support. So if you have a JMicron-controller for 2 "extra" ports, you also have at least 4 to 6 SATA connectors provided by ICH9R chip; and that one supports RAID at high performance.

Intel has the best RAID drivers; but like JMicron this also is pure driver RAID - no "hardware acceleration" is performed!