Typically I do
1. Make sure BIOS setting for RAM are set to manf spec
2. Memtest overnight, 8 passes min.
3. Install OS
4. Get online and DL and install latest Chipset and video drivers
5. Update Windows.
6. Install antivirus, firewall and threatfire.
7. Install Everest (or free equivalent would be CPU -Z, GPU-Z and HW monitor)
8. OC and tweak CPU.
9. Insure stability of final OC with 12 hr Prime 95.
10. OC and tweak RAM. Round 2 of Memtest 8 passes after final OC.
11. OC and tweak GPU
12. Furmark for GPU stability. 2-3 hr run.
13. Rivatuner + speedfan to tweak fan profiles.
14. Rest of stuff the software.
BIOS flash isn't necessary unless there's an issue or new feature you want. Avoid in windows BIOS flashing. Always flash using a bootable disk.