Use KERNCONF=CUSTOM to designate a custom kernel in both buildkernel and installkernel steps. Omit for a GENERIC kernel.
# cd /usr/src # make buildkernel KERNCONF=CUSTOM # make installkernel KERNCONF=CUSTOM
Many people find it useful to keep the kernel config file elsewhere and use a symbolic link from the appropriate directory. In this example using /usr/src/sys/i386/conf:
# cd /usr/src/sys/i386/conf # ln -s /root/kernels/CUSTOM
This makes it easy to entirely remove /usr/src if ever necessary and not lose your kernel configurations.