Hey jeffunity,
For the sorting, check the Frontpage template in your template builder and expand the options for the Portfolio. There should be options to control that portfolio there instead of in the theme options.
The portfolio won't crop your images by default to keep the portfolio all exactly aligned. Its set to just shrink them down to the width and let the height adjust proportionally. To change this, open your functions.php in your theme files and look for:
$avia_config['imgSize']['portfolio'] = array('width'=>448, 'height'=>330 ); // images for portfolio entries (2,3 column)
Change it to:
$avia_config['imgSize']['portfolio'] = array('width'=>448, 'height'=>330, 'crop'=>true); // images for portfolio entries (2,3 column)
Save the file then use this plugin to regenerate your thumbnails: http://wordpress.org/extend/plugins/regenerate-thumbnails/
I've sent an email to the head of support re the sorting issue and will update once I hear back.
Regards,
Devin