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CREATE TABLE USER_BRANCH_XREF (
    USER    VARCHAR2(20)  NOT NULL  REFERENCES USERS(USERNAME)
   ,BRANCH  NUMBER        NOT NULL  REFERENCES BRANCHES(ID)
   ,CONSTRAINT PRIMARY KEY (USER, BRANCH)
);

SELECT branches.id    AS value
      ,branches.name  AS branch
...
 WHERE users.username = ?
   AND user_branch_xref.user = users.username
   AND user_branch_xref.branch = branches.id

my $sql = <<__END_SQL__;
SELECT branches.id    AS value
...
$template->param(
    branches => $sth->fetchall_arrayref( {} ),
);