Easier Solution
The best way I can think of is to offer an alternative-view of the text, a printer-friendly version that doesn't show your post-it boxes. As long as the content of the post-it is within the text-flow, you're going to have this issue.
Potential (More difficult) Alternative
As a more difficult alternative, you could go a javascript route. It would involve inserting an empty DIV in the main text and giving it a set width and height, then placing the post-it over that same location with absolute positioning.
<div id="container" style="position:relative;">
<div class="text">Duis non lorem vel diam adipiscing dignissim.
Nulla vel varius erat. Nulla facilisi. Vivamus pulvinar pretium dignissim.
Aliquam sed tortor posuere nunc bibendum mattis. Integer bibendum, elit ut
vestibulum tristique, dolor justo scelerisque nibh, ac blandit metus arcu
non nibh.In ac eros sed nisl porta bibendum quis in mauris. Quisque
<div style="float:right; margin:10px; width:100px; height:100px;"></div>
pellentesque ligula eu sapien commodo at mollis purus feugiat. Vivamus
volutpat dictum magna eu venenatis. Suspendisse dignissim enim aliquet leo
imperdiet vitae accumsan mauris blandit. Donec tempus velit aliquet magna
imperdiet euismod. Lorem ipsum dolor sit amet, consectetur adipiscing elit.
Vestibulum mollis tortor pellentesque velit pharetra non lobortis est
aliquam.
</div>
<div class="post-it">
I am the post-it. I should be placed absolutely so that
I overlap the div that is presently sitting within the body of text. This
will give the impression that I too exist within there, but I won't be
selectable.
</div>
</div>
Dynamically determining the width/height of the empty-div so that it matches that of the post-it can be pretty easily done with javascript. Here's an example using jQuery:
var realWidth = $("#container > .post-it").width();
var realHeight = $("#container > .post-it").height();
$("div.text div:eq(0)").css({"width":realWidth,"height":realHeight});
Then you'd want to get the x and y offset of the empty div, and apply that as the left and top values of the post-it div, so it sits right on top of the text, in the designated area.