For windows, you will need a bootable USB stick.
Read this
EDIT: http://rufus.akeo.ie/
And ofc, write down your CD key, on paper!
THe relevant data for you would be in My Documents Folder + Desktop + Downloads (or under the Users in the Primary Partition (OS that is)). Just copy + paste it onto the other hardrive. (You can also choose Windows backup if u want your Outlooks conversations saved and every other settings, but this can take up to a few hours - Personnaly, I never did this!)
If you have any saved games, they are usually saved smwhere under My Documents too, so you should be safe.
As a piece of advice: when u start the fresh install, format (and partition, if u want/need) the entire drive (dont do this unless you already have more than one partition on the OS hardrive and you want to keep the data on the those other partitions. Eg: OC (C), Data (D), Data (E) - in this case, format only C.) Full format is always better ( I know from my personal experience).
After you make the bootable stick, go into BIOS and change the booting priority, so it boots from USB. If it doesnt, than your priority is not right yet OR the USB stick is not bootable. After you have installed the OS (when u arrive to 1st reboot, if i remember corectly, change the priority to normal again (or just remove the USB stick)).
Usually these things go smooth.
Dont forget to have some drivers saved on an external USB (other than the win 7 one) or on an external HDD or something. Atleast the Lan/Wireless drivers. This will allow you to connect to the internet in order to get the newest drivers online.
Goodluck