Since distro-provided driver binaries aren't really an option when using a custom kernel, it's necessary to do things the vendor way. Thankfully, this typically provides better results than precompiled binaries anyway. On true Debian distros1), I recommend sgfxi for easy video driver installation. sgfxi will automatically identify your video hardware, grab the very latest working driver from the appropriate site, patch it against your kernel if necessary, build it and install it neatly. Installing it is also exceedingly simple.
First, get root:
su -
Then download sgfxi to a place in your path:
wget smxi.org/sgfxi -O /usr/local/sbin/sgfxi
Next, make the script executable:
chmod +x /usr/local/sbin/sgfxi
Finally, run it:
sgfxi
In my case, I prefer to run common maintenance tasks with sudo rather than needing to drop to root each time. In that case, you'd simply give yourself sudo rights to run sgfxi:
Get root:
su -
Edit the sudoers file using 'visudo':
visudo
…then add something like the following line:
%video ALL=/usr/local/sbin/sgfxi
That would give sudo access to recompile the video drivers to any user belonging to the 'video' system group. If you only wanted your own user account to have sudo rights to run sgfxi, you could drop the % and replace 'video' with your own username. Once finished, save the file and exit. Visudo will inform you if you've made a syntax error. Next, drop root privileges, you don't need them anymore:
exit
From now on, you can run sgfxi via sudo from your normal user account:
sudo sgfxi