Setting up new chapters and stories
Working with the manuscript as is isn't as difficult as it sounds. The purpose of putting the pages alongside each other is purely so you can see where to insert page and section breaks. If you want you can insert a blank page at the beginning of the document as its own section, which will at least make everything look as if it's in the right place. But you'll need to take it out before you do your table of content, and reverse left and right in my posts, so I really wouldn't recommend it.
If you look at a traditionally published book you'll see that new stories and chapters begin on the right hand page, even if this means having a blank page on the left. This is a convention you'll need to follow if you want your self-published book to appear professional. If you're printing only for friends and family you may not be bothered by this, in which case feel free to start new chapters on the next page.
If you're starting new chapters/stories on the right hand page, this means that they need to start on the left in the Word document. All you need to do here is insert a page or section break, or two, to get the new text in the right place.
Whether you choose a page or section break depends on if you want your headers or footers the same throughout the main body of text. If you want them the same, choose a page break. If they're different (for example to put the title of individual stories their own title as header) you need a section break. More on that in my next post.