If I understand you correctly, you just need to set 2 different array_ref parameters in your HTML::Template object, and then have 2 TMPL_LOOPs in your template. Pseudo-code to illustrate:
# in your script.pl
my $tbl1_array_ref =
$dbh->selectall_arrayref($sql_tbl1, {Slice=>{}}, @bind_values);
my $tbl2_array_ref =
$dbh->selectall_arrayref($sql_tbl2, {Slice=>{}}, @bind_values);
$tmpl_obj->param( TABLE1_DATA => $tbl1_array_ref );
$tmpl_obj->param( TABLE2_DATA => $tbl2_array_ref );
<!-- in your template.tmpl -->
<TMPL_LOOP TABLE1_DATA>
<TR><TD><TMPL_VAR ESCAPE=HTML COLUMN1></TD></TR>
<!-- yada yada yada -->
</TMPL_LOOP>
<TMPL_LOOP TABLE2_DATA>
<TR><TD><TMPL_VAR ESCAPE=HTML COLUMN1></TD></TR>
<!-- yada yada yada -->
</TMPL_LOOP>
HTH
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