Are you saying you have 2 hard disk drives? If your after formatting your PC use the XP installation CD to format and reinstall windows.
Did you get an identical motherboard to the previous one or is it a new motherboard?
FYI- you shouldn't need to format both disks. If you have something you want on the one without windows on it, it will still work without formating it.
I doubt that your eMachine 2 disc set will work anymore.
Due to Microsoft's OEM/EULA (License Agreement), when you installed a "New" motherboard rather than an eMachine replacement, you basically bought a "New" PC and your Installation disc's for the eMachine will not install or it will install, but when you go to activate it using the eMachine product key, MS will deny activation stating the key is invalid.
There's still hope in that scenario, assuming you get Windows installed and then activation is denied, all you have to do is call Microsoft, explain that you own the PC and had to have the motherboard replaced and in most if not all cases they will issue you a new key free of charge.
The down side is what I mentioned before, it might not install at all.
Give it a shot and hope it works out for you.