I suggest to use javascript:
This is to open the popup window. The important thing is that the new window is an object called "nw". Create it and name it as you wish, but that's the important stuff so...
<input type="button" value="create popup" onclick="nw=window.open('theFrameset.htm','_blank');" />
...You can easily access its properties and elements:
<a href="#" onclick="nw.document.getElementById('frame1').src='thisGoesInsideTheFrame.htm';">fake link</a>
And this is how the code for the popup window may look like:
<frameset>
<frame name="frame1" id="frame1">
<frame name="frame2" id="frame2">
</frameset>