You either assume that there is ALWAYS a header, or that any header will be commented by some character, I will show you the first. You can just wrap the insertion lines in a conditional block to check for this.
if( $lines != 0 ) // or $linemysql[0][0] == '#' (assuming # is a "comment")
{
if($addauto)
$query = "insert into $databasetable values('','$linemysql');";
else
$query = "insert into $databasetable values('$linemysql');";
}
That being said, PLEASE! Do not ever use the code you posted in any internet facing application, you are putting user-provided data directly into the database, so it would be trivial to make a csv file containing SQL injection attack and change your mysql password, steal your data, kill your cat or delete everything. You should also check the number of fields and such, what happens if the csv contains lines without the correct number of fields ?
Read up on http://en.wikipedia.org/wiki/SQL_injection and also http://php.net/PDO