Alright, I worked out a way to do this, so I thought I should share.
As the slides are matched index wise, I just needed to make the jQuery Cycle current slide match which ever slide index is currently being displayed by supersized, with this function:
window.matchSlides = function()
{
$j('#subBanner').cycle(vars.current_slide, 'fade');
}
The function is then called by beforeAnimation in my theme file (checking to see if the function exists - as I use this plugin in other sections of the site without this requirement as well:
if(typeof window.matchSlides == 'function') {
window.matchSlides();
}