You're going to get in an awful mess trying to do this with regex. It's very simple to loop through the characters of a string and do this kind of checking. Something like the following should work:
<?php
function specialsplit($string) {
    $level = 0;       // number of nested sets of brackets
    $ret = array(''); // array to return
    $cur = 0;         // current index in the array to return, for convenience
    for ($i = 0; $i < strlen($string); $i++) {
        switch ($string[$i]) {
            case '(':
                $level++;
                $ret[$cur] .= '(';
                break;
            case ')':
                $level--;
                $ret[$cur] .= ')';
                break;
            case ',':
                if ($level == 0) {
                    $cur++;
                    $ret[$cur] = '';
                    break;
                }
                // else fallthrough
            default:
                $ret[$cur] .= $string[$i];
        }
    }
    return $ret;
}
var_export(specialsplit("string1 (sString1, sString2,(ssString1, ssString2)), string2, string3"));
/*array (
  0 => 'string1 (sString1, sString2,(ssString1, ssString2))',
  1 => ' string2',
  2 => ' string3',
)*/
Note that this technique is a lot harder to do if you have more than a one-character string to split on.