As I stated you can save your files to another drive, a second internal or external usb/sata/firewire drive using the W7 ETW.
"could i switch everything to another hdd and then reconnect it after the fresh install and then switch what i needed to back onto the primary hdd ?"
NO! You CAN NOT move the programs from one drive to another and back again.
Use the second drive to store the backup file made by W7 ETW, then restore it back after you have completed the upgrade.