The Source Engine's controller support never felt right to me. I use something called "AntiMicro" which is an open source keyboard/mouse mapper, but it's features and simplicity easily rival the paid apps available on the internet. I actually have a paid for version of Pinnacle Profiler, but I prefer Antimicro for it's natural feel when playing games. Here's the link:-
https://github.com/AntiMicro/antimicro/releasesDownload the "Portable" version if you don't wish to install. All you need to setup is the control sticks, you can set your controller buttons in Goldeneye Source. I have spent a long time creating the best, most natural feel for my controller and have taken some screenshots of my right stick settings as a guide for you:-
This is the main menu, as you can see, I have set a controller button as MouseLB, this is so I don't have to use the mouse on the menu's. Also, I have set START button as Escape, again to make menu navigation possible on the controller.
Once you have set those two buttons, click on "L Stick" and set the left stick to "WSAD" for the keyboard, adjust any sensitivity settings to your personal feel on this one, I left them at default.
Now the Right stick...
These are my settings, You may wish to tweak them to your personal preference.
Once your done here, click on "Mouse Settings"...
Set your settings as you see above.
FINALLY... You will need to set your mouse speed in Goldeneye Source menu quite high, Anywhere between 6-8.0 depending on what feels good to you. I found that this balance of low in AntiMicro, and high in GE:S to feel really smooth.
IMPORTANT. Make sure you have controller unticked under Goldeneye Source Mouse Settings menu.
I hope this helps, any questions just ask.