You should be able to use your key board and mouse in conjunction with your controller. I can't test it myself but if it's not working we may need to add the background keyboard and mouse settings back to the INI. If that doesn't work we''ll have to wait a bit and see if maybe SKSE can ease the woes. If that doesn't work do as i do and use a programmable gamepad that emulates the keyboard and mouse and learn to use all three.
This most definitely does not work out of the box. I use a 360 controller, and as long as it's turned on, the mouse and keyboard does absolutely nothing in game (except for arrows navigating menus, strangely).
It really svcks because I want to use my keyboard for some things and my controller for most things, but it doesn't work.