Here's my take on it. I added CREATE TABLE and altered the beginning a little:

#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper::Concise;

package MyDictionary::DBI;
use base qw(Class::DBI::SQLite);

our (%SQL_CREATE);

__PACKAGE__->set_db( 'Main', "dbi:SQLite:dbname=Dictionary.db", , );

package MyDictionary::Engword;
use base qw( MyDictionary::DBI );

$MyDictionary::DBI::SQL_CREATE{englishwords} = "
CREATE TABLE englishwords (
    skword
    engword
  );
";
MyDictionary::Engword->table("englishwords");
MyDictionary::Engword->columns( Primary => qw/skword engword/ );
MyDictionary::Engword->has_many(
    sort => [ 'MyDictionary::En_To_Sk' => 'skword' ],
    'engword'
);

package MyDictionary::Skword;
use base "MyDictionary::DBI";

MyDictionary::Skword->set_up_table("skwordmeaning");
MyDictionary::Skword->has_many( sort =>
    [ 'MyDictionary::En_To_Sk' => 'engword' ], 'skword' );

package MyDictionary::En_To_Sk;
use base "MyDictionary::DBI";

MyDictionary::En_To_Sk->set_up_table('en_to_sk');
MyDictionary::En_To_Sk->has_many('eng_id' => "MyDictionary::Engword");
MyDictionary::En_To_Sk->has_many('sk_id'  => "MyDictionary::Skword" );
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