Have you considered letting the method calls return the object?

google.com/search?q="return the method" site:www.perldoc.com
A quick read of the Data::Dumper source later;
Wow, thanks, that works great!

There is a lot more I would like to implement, but at the moment I'm constrained by the specific requirements of the project I'm doing at work, at what functionality the module needs for that. - Unfortunately, it'll very much be a 'add it as it's required' approach.

I will be looking further at your other suggestions though, thanks!

For now however, I've changed it so that doing,

use strict;
use warnings;
use SQL::Builder::Select;

my $select = new SQL::Builder::Select;

$select->column( '*' )
       ->table( 'main' )
       ->where_ne_or( 'col1' )
       ->where_eq_and( 'col1', 'col2' )
       ->where_logic( 'a and o')
       ->order_by( 'col1' )
       ->limit_value( 10 )
       ->limit_offset( 20 )
       ->debug( 1 );

print $select->return();
[download]

DEBUG: logic broken up
    'a ', 'AND', ' o'
DEBUG: joining
    AND - 'col1 = ?', 'col2 = ?'
DEBUG: no need to join
    'col1 != ?'
DEBUG: joining
    AND - '(col1 = ?) AND (col2 = ?)', 'col1 != ?'

DEBUG: sql
    SELECT * FROM main WHERE ((col1 = ?) AND (col2 = ?)) AND (col1 != 
+?) ORDER BY col1 LIMIT 20, 10
[download]