It's sloppy, but you could also have 3 includes for 2 different stylesheets.
1.) First include defines your entire site layout and such
2.) Second include is just before the WYSIWYG editor, and includes the WYSIWYG stylesheet
3.) Third one is after the WYSIWYG editor and is another inclusion of the original stylesheet.
Like I said, sloppy, but it should work.
Now, the proper way to fix this is to change your CSS so it doesn't interfere with the WYSIWYG editor. You can do this in one of two ways:
1.) Just flat out change your CSS declarations (case-sensitive. So input != Input != iNpuT)
2.) Wrap the WYSIWYG editor in a div (with no style) and change the WYSIWYG editor definitions so that they are only relevant to when it's inside that specific div:
<div id="wysiwyg_editor">
<!-- Your WYSIWYG editor controls -->
</div>
#wysiwyg_editor .common_class_name {
/* Declarations */
}
Now, you can limit even further by adding a ">" in between "wysiwyg_editor" and ".common". Play with it until you get it right if you do that.