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Just a quick note so I don’t have to look this up all the time.
From a vanilla Debian base box (the NetInstall, or similar), we’ll need the basic build-essential and make packages. apt-get install them. We’ll also need git, which is less likely to be installed be default.
The first order of business is figuring out what hardware you’ll be targetting. This is ARM, i386, x86_64/amd64, etc. Shouldn’t be too difficult to determine.
The second order of business is obtaining the kernel. If you’re cross-compiling, then you’re more likely to be wanting a fork of the kernel from somewhere. Right this minute, I’m looking at compiling a new Kernel with some specific options for a Raspberry Pi. They’re got their own repo for now. Someday down the line, it might end up being merged back into Mainline Linux, which would be at kernel.org (download/git links at the bottom of the page).
So either checkout/branch to the version you want, or download and untar it to your home directory. It’s generally not recommended to be running as root for any compilation action, including any sudo actions, so there’s no reason in needs to be in /usr/src. If you recompiling your kernel for the machine you’re running on that’s a different story.
Set an environmental variable to the base location, export KERNEL_SRC="$HOME/src/linux", and cd into it: cd $KERNEL_SRC.