I have sort of answered my own question. Instead of using a popup or menu I have put the filter buttons in a second isotope instance by following this answer by hyde
I modified Hyde's example of multiple isotope instances on Fiddle
check out my fiddle
I'm still tuning it but the basic idea (of retractable filter button groups) is working.
<!-- first filter buttons -->
<section id="options" class="clearfix">
<h3>Filters</h3>
...
</section>
<!-- end first filter buttons -->
<!-- first filter container -->
<div id="container" class="container clearfix">
<--! second filter buttons -->
<section id="options-new" class="clearfix">
<h3>Filters</h3>
...
</section>
<!-- second filter buttons -->
</div>
<--! first filter container -->
<--! second filter container -->
<div id="container-new" class="clearfix">
...
</div>
<--! second filter container -->
I'm still open to input on refinements!! :)