Yes, when you install a new custom ROM, in 99% of cases, it will overwrite/install a new kernel that comes with the ROM.
Why is this?
This is because ROMs come with kernels. Kernels are part of the ROM in essence. However if you want to run another kernel, it’s simple as flashing your desired kernel over the ROM in ClockworkMod Recovery after installing ROM.
Also, kernels must be compatible with the ROM you are installing.
In most cases, Gingerbread kernels are only compatible with Gingerbread RO