Anyone know about modding sys files?

i'm on x64. i've been tweaking shell32 and i ran into an odd issue.. if i replace the file in system32 and in syswow my system throws errors (i think runtimes or something) at log in and things get weirder after that. but if i keep syswow unmodified and change only system32 i get no errors and everything appears to work as intended. from my brief research, i was to understand that you needed to replace both, but when it threw errors i tested the a fore mentioned method and it works fine, so far.

if anyone knows about this stuff please let me know. if you want to chat i use skype or you can find me on facebook @ facebook.com/aaron.a.fb

any help is greatly appreciated. i haven't really res hacked anything since my xp days, and even then i was poking around blindly. with windows 8 coming in the next couple of months, reshacking should be pretty popular for a bit, and i'm eager to learn