Hello crownpiyush,
It is recommend to Update your BIOS only if there is something positive for you to gain from the update. (Example: You have check your video card in another computer and it works fine but it refuses to work in your own system even after disabling onboard BIOS and selecting PCI-e as the Graphics card BIOS boot option. If a new BIOS exist, installing it could possibly resolve that issue.) Do not try to fix something that ain't broken...! If your computer meets your expectations, than leave it alone and enjoy it. Remember that the onboard video is fine for 2D operations. If you intend to play games or view HD videos you will have to get your Video Card back into your sysyem to do so.
I cannot assess your boot time unless unless you post your system particulars in you signature block as requested earlier. Give actual boot times not feelings. Your Seagate Hard drive will be fine in either one SATA ports. Both SATA ports can handle more than its max output. Also I suggest that you be specific when you talk about a device, give common name and part number. Check the seagate website for a possible firmware update for your hard drive. Remember to backup your hard drive before applying any firmware update to it.
There maybe one explanation for your longer than expected boot time. You appear to have selected some RAID options in BIOS and you appear to have only one hardrive. Your BIOS and your RAID driver may be looking for a RAID array during the Boot sequence. Make sure that Full Logo boot option is disabled so that you can see the various BIOS screens during the Boot process. Watch at the top of the second or third boot page for something about RAID or locating a RAID array. If you do have only one hard drive turn RAID off and Select IDE mode.
You should also enable the Quick Boot option in BIOS.
Cheers...