got SA2K running 6.0R10 (build 13911) can i upgrade it directly to 6.3r3 without loosing configuration?
Yes. But I'd still back up the system and users config before you do it.
Also, you may want to deploy the Juniper Installer Service for the new OS, to your clients ahead of time. This let's them install the upgraded components w/o admin rights.
Deacon very good advice. Always backup and yes i have upgraded from 5.5 to 6.3r3 without any issues