I used CentOS 5.5 for working on the NetFPGA. I haven't tried Fedora but the same commands should work for Fedora too (atleast for Fedora14). For installing the OS, you can follow the instructions here :http://www.howtoforge.com/installation-guide-centos5.1-desktop
The different pages on this link give an idea to install the CentOS step-wise and following these instructions can make the installation simpler.
Note the following while the installation is in progress :
1. Do not install Virtualization as we require a full installation of OS on hard drive.
2. Set SELinux to : Not Enforcing (otherwise you will need to adjust the security settings manually)
3. Disable the firewall
4. Attach your eth0 (motherboard's primary interface) to the external network
5. It is easiesr to use DHCP to set the IP address, gateway, DNS
After the installation, the Package Updater will prompt for an update. Ignore it as installing the updates now will result in missing dependency issues later while installing the Java GUI.