markos The easiest way is probably to follow the packaging guide. You can skip the "Setting up a Dev Tracker Account" section if you don't intend to submit package changes. Once you've done that, clone the kernel package with make linux-current.clone (or linux-lts if you want the LTS kernel). All the kernel config stuff will be in the files subdirectory. After you've made your changes, you can build the package with make.
Note that if you use any out-of-tree kernel modules (such as nvidia, broadcom, virtualbox, etc.), they will also have to be rebuilt against your kernel. See this article for more details about that. A file in the kernel package lists the rebuild order.
The repository for the kernel package can be found online here.
