Puoi modificare la struttra della tabella mettendo le informazioni che vuoi all'interno del riquadro in un unico TD impostando rowspan e colspan.
Vedi se così fa per te.
codice:
<html>
<head>
</head>
<body>
  <table align="center">
    <tr>
      <td>Totale 1</td>
      <td><input name="Tot1" maxLength="30"  size=10 style="background:#CCFFFF ;" readonly> <input name="Commento_Tot1" type="button" value="*" onClick="show_hide(this);"> </td>
      <td colspan="2" rowspan="2" style="border:1px solid red;">
        X <input name="X" maxLength="5"  size=6 style="background:#FFFF00 ;" readonly> <input name="Commento_X" type="button" value="*" onClick="show_hide(this);">

        Y <input name="Y" maxLength="5"  size=6 style="background:#FFFF00 ;" readonly> <input name="Commento_Y" type="button" value="*" onClick="show_hide(this);">
      </td>
    </tr>
    <tr>
      <td>Totale 2</td>
      <td><input name="Tot2" maxLength="30"  size=10 style="background:#CCFFFF ;" readonly> <input name="Commento_Tot2" type="button" value="*" onClick="show_hide(this);"> </td>
    </tr>
    <tr>
      <td>Totale 3</td>
      <td><input name="Tot3" maxLength="30"  size=10 style="background:#CCFFFF ;" readonly> <input name="Commento_Tot3" type="button" value="*" onClick="show_hide(this);"> </td>
    </tr>
    <tr>
      <td>Totale 4</td>
      <td><input name="Tot4" maxLength="30"  size=10 style="background:#FF0000  ;" readonly> <input name="Commento_Tot4" type="button" value="*" onClick="show_hide(this);"> </td>
    </tr>
  </table>
</body>
</html>