"But my new motherboard is a different brand"
Did you check for compatibility? CPU, RAM, onboard sata support, etc.?
"do you think I need to install windows from the begining?"
No, because windows is on the HDD, which I assume you didn't replace.
"Or will it work smoothly?"
It's not a software issue. Since your MB changed, is your hardware compatible? Or you won't be booting up.
"If not how can I save my files?"
Take out the HDD, and use it with another working comp, either as an internal, or wrapping it in an external enclosure.