[Plugin: WP-Paginate] posts_per_page with custom queries

I am doing search queries with custom fields and other custom tables. For example:

SELECT DISTINCT wposts.*
    FROM $wpdb->posts wposts, $wpdb->postmeta wpostmeta
    WHERE wposts.ID = wpostmeta.post_id
    AND
    (
    	wpostmeta.meta_value regexp '$s'
	OR wposts.post_title regexp '$s'
    )
    AND wposts.post_status = 'publish'
    ORDER BY wposts.post_date

I have the $paged variable set, but I am getting the whole result in one huge page, like 100+ posts. Is there a way to manually set the posts_per_page value? Some variable maybe? wp-paginate is not handling this right now.

Thanks.