Can you say a little more about your problem? It's not clear from the explanation above exactly what you're trying to do. Are you trying to get the values from the array of check boxes in a controller, and assign them to a different set of parameters?
Are you trying to do something in the page itself (maybe with JavaScript) to cause one set of check boxes to act on a different set of check boxes in the same page?
What do your parameters look like (in the development console) when you submit this form?
Walter