Copying and pasting from the Devil's typewriting program (Word) is, as you have found, problematic. There are some formatting options within Word that will never copy across. If you copy direct into the editor window then M$'s junk style code will be copied too, and on saving the codesweeper may well remove any formatting that is not correct XHTML - even then you are likely to end up with junk like
<p class="MsoNormal">
<span style="font-size: 10pt; font-family: Arial"><span> </span><span lang="EN-US"></span></span>
</p>
So it is better to use the pop-up pasting option for Word. This at least loses the M$ junk code. Some text formatting - paragraphs, bolding, lists etc will copy OK, but tables, for example, are likely to fall apart. Also there may still be some M$ in-line styles there which will over-rule your page CSS.
I rarely paste directly from Word - my usual way is to copy from the document into NoteTab Pro (any good plain text editor will do), then copy and paste from there into the editor, and re-add the formatting. This picks up my styles and ensures consistency.