HI timekills,
I personally just use the default keyboard assignments at the moment and keep an extra keyboard handy for any additional things that I need. I may consider using a g13 that I have or getting a second button and controller set,(something cheap), to setup special commands. You will have to forgive me for lack of detailed information as I am still working things out myself. I have suggested to X-arcade that they make some software like the logitech keyboard software that is application aware and can be programmed on an application-by-application basis to make things easier for using the wide variety of emulators that we use. Who knows maybe someday
I will say that I try to keep in mind that keys like esc, tab, and the f-keys can sometimes have special functions in applications so I stay away from assigning them to my controller unless I am absolutely sure that they will not interfere with the applications. Also don't forget the shift+, special character, and punctuation keys when you need something a little different.
Hope this points you in the right direction. Happy gaming.
Maozem