I am (very) possibly wrong, but I think that this should be simpler than it sounds.
This was already mentioned, but... use "su
Open a terminal. Type "su" (without quotation marks). <enter>. Type in the adequate password. <enter>.
Now type the command you want/need. For example, type "nano" (without quotation marks) and press <enter>. With nano, open your file, edit it, save it.
After changing the config file, if conky still doesn't work as you intended, try, just in case, saving your session and logging in again. Still not good enough? Go "crazy"
and close the OS and reboot.
Again, it is very possible I am wrong somewhere in this post (or even entirely wrong). In any case, please report back.