I assume you have a x32 (also seen as x86) version of windows as well as a x64 version of it? You do not need the non 64 one, but it is nice to also have the other for some compatibility issues. The program is rather small so unless you have a really tiny hard drive do not worry about it.
If you are talking about two different version of IE then simply uninstall the older version. If you need help on how to do this or my answer does not answer your question let me know.