# @where_clause has been fully defined

my $query = "SELECT * FROM $table WHERE ";
$query .= join " AND ", @where_clause;

my $sth->prepare( $query ) or die #stuff;
$sth->execute( ) or die #stuff;

##</code><code>##

# From your code above:
if (defined($allocated_to) && $allocated_to ne '') {
push @where_clause, "UPPER(ALLOCATED_TO) LIKE UPPER(?)";
push @entries, 'ALLOCATED_TO';
push @values, '\%$allocated_to\%';
} 
#
# yada yada yada
#
my $query = "SELECT * FROM $table WHERE ";
$query .= join " AND ", @where_clause;

my $sth->prepare( $query ) or die #stuff;
$sth->execute( @values ) or die #stuff;