You can have as many kernels as you want.
What you did was...
make modules modules_install. This overwrites /lib/modules/2.4.X
Once you have re-installed the nvidia driver it will work in both kernel as long as they share the same /lib/modules in other words if they are in fact the same kernel but with differrent options built.
If you want to compile different kernel versions, You will have to boot the new kernel and install the kernel module so that it is in the new /lib/modules/2.4.XX.