I have figured it out! I placed this code at the bottom of the script and it sorts both sheets before creating the file and saving it.
$Range1 = $Sheet1.range('A2:D2500')
$Range2 = $sheet1.Range('B2')
$Range1.Sort($Range2, 1)
$Range.entirecolumn.autofit()
$Range1 = $Sheet2.range('A2:D2500')
$Range2 = $sheet2.Range('B2')
$Range1.Sort($Range2, 1)
$Range.entirecolumn.autofit()