May I know what configurations are done on the motherboard when it is a newly purchased motherboard.The changes I am referring to is physically and through the software.Just to give me an idea of the things done to a brand new motherboard

I would do no changes until you are sure the thing works as it should. If you mess about with set up and the like and you have a problem you will not know what caused it.

really the only software thing you can change on a motherboard is the BIOS..you can flash it... but if your not having any problems then it is not recommended.. especially because if you mess up and the flash goes wrong you will have to take you mobo to a comp shop where they can install a new bios on it....and that takes $$$$

if it has jumpers, you might need to set stuff up like clock speed (mine is jumperless, except for one jumper which is used to clear cmos). otherwise, nothing else needs to be done to get it ready. for software, you'll need to install the motherboard's chipset drivers on the computer you're going to use it on. you might want to flash the bios if the mobo was made a while back and hasn't been updated (so that it can use faster cpu, etc...) but flashing bios is dangerous if you mess up...your computer will need to be started in order to fix a bad bios flash, but you can't start up your computer until you do fix it (paradox).