editing files is nothing amazing, feel free to do it (if you know what your doing), or first backup the original file then edit it (if your not sure)
anyway, as for when changes take effect, it all depends on the program
programs like lilo uses the config file to setup the boot loader, each time you want to update the boot loader (if you upgraded, or made a change to its config file) then you must run the program before it'll take effect
but for most, one should assume changes only take effect on program restart (as config files are usually read at startup of the program)
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