What I did was first look at the default assignments in the game and write those down. Then in pinnacle I made the entire list of commands with labels. So I would make a command called "Jump" and assign it to the space bar in Pinnacle.
This way if you want to play with the k/m at some point your button assignments are still default. Also, if you ever have to delete your config file for some reason you don't have to completely re-assign the buttons in the game.
Once I had all the commands in my command list in pinnacle I started making the profile.
My profile has all of the commands in the game already setup using the games default keys so if you wanted you could load my profile. You can then delete my controller config and start making your own for an xbox controller.
In order to access all the menus easily I recommend using a shift button. So my D-pad is normally inv/map/skills/quests but if I hold down my left trigger (shift) the d-pad becomes save/load/quick save/quick load. The same is for my 1-4 buttons (or x,y,a,b for you). They are the 1-4 quick slots normally, then shifted they are 5-8.
Hope this helps!