An example plugin to show the use of the PHP SPL and subsidiary loops with a FilterIterator.

MinFilterIterator.php

<?php
// Reduced to the minimum
class ThumbnailFilter extends FilterIterator
{
	private $wp_query;
 
	public function __construct( Iterator $iterator, WP_Query $wp_query )
	{
		NULL === $this->wp_query AND $this->wp_query = $wp_query;
		parent::__construct( $iterator );
	}
 
	public function accept()
	{
		$this->wp_query->the_post();
 		$this->wp_query->current_post === $this->wp_query->query_vars['posts_per_page'] // -1
			AND $this->wp_query->rewind_posts();
 
		return $this->wp_query->have_posts() AND $this->deny();
	}
 
	public function deny()
	{
		return ! has_post_thumbnail( $this->current()->ID );
	}
}

WP_QueryFilterIterator.php

<?php
/**
 * Plugin Name: (#130009) Merge Two Queries
 * Description: "Merges" two queries by using a <code>RecursiveFilterIterator</code> to divide one main query into two queries
 * Plugin URl:  http://wordpress.stackexchange.com/questions/130009/how-to-merge-two-queries-together
 */

class ThumbnailFilter extends FilterIterator implements Countable
{
	private $wp_query;

	private $allowed;

	private $counter = 0;

	public function __construct( Iterator $iterator, WP_Query $wp_query )
	{
		NULL === $this->wp_query AND $this->wp_query = $wp_query;

		// Save some processing time by saving it once
		NULL === $this->allowed
			AND $this->allowed = $this->wp_query->have_posts();

		parent::__construct( $iterator );
	}

	public function accept()
	{
		if (
			! $this->allowed
			OR ! $this->current() instanceof WP_Post
		)
			return FALSE;

		// Switch index, Setup post data, etc.
		$this->wp_query->the_post();

		// Last WP_Post reached: Setup WP_Query for next loop
		$this->wp_query->current_post === $this->wp_query->query_vars['posts_per_page'] // -1
			AND $this->wp_query->rewind_posts();

		// Doesn't meet criteria? Abort.
		if ( $this->deny() )
			return FALSE;

		$this->counter++;
		return TRUE;
	}

	public function deny()
	{
		return ! has_post_thumbnail( $this->current()->ID );
	}

	public function count()
	{
		return $this->counter;
	}
}

class NoThumbnailFilter extends ThumbnailFilter
{
	public function deny()
	{
		return has_post_thumbnail( $this->current()->ID );
	}
}

add_action( 'loop_start', 'wpse130009Query' );
function wpse130009Query()
{
	// Only need to remove this callback for the current test
	// Else we'd infinitely nest this callback as WP_Query::the_post()
	// calls the 'loop_start' filter.
	remove_action( current_filter(), __FUNCTION__ );

	global $wp_query;

	echo number_format_i18n( $wp_query->found_posts );

	$arrayObj = new ArrayObject( $wp_query->get_posts() );
	$primaryQuery = new ThumbnailFilter( $arrayObj->getIterator(), $wp_query );
	$secondaryQuery = new NoThumbnailFilter( $arrayObj->getIterator(), $wp_query );

	foreach ( $primaryQuery as $post )
	{
		var_dump( get_the_ID() );
	}

	foreach ( $secondaryQuery as $post )
	{
		var_dump( get_the_ID() );
	}
}

@samjco You can find plenty of examples on StackExchange sites and StackOverflow themselves as well as various blogs. For the reasoning, read for example this SO answer. The filters explain themselves if you look at their code above. They wrap basic WP functions that you can look up at WPs dev resources. Hope that helps.

Ok, so the main goal is to first define one query with all args. Then from there, you can remove args using deny(), thus making the main query into 2 queries. First (the main) query results, of all desired args, and the other query results are with less-than all args as - we take things out using the function: deny()... Thus splitting the query into two.
Is this correct?

@samjco Yes, you got it. Save DB-queries and just split the the data set into multiple loops, easy and readable.

So then the class "ThumbnailFilter" and "NoThumbnailFilter" can be named "FirstQueryResults (or MainQueryResults)" AND "SecondQueryResults"...
I will also attempt to make a real-life example for others who were stumped like me...

Another question...
Doesn't this show each query results in one after another instead of mixed in together?
So in order words... The $primaryQuery results all shows first and then $secondaryQuery's results:

	foreach ( $primaryQuery as $post )
	{
		var_dump( get_the_ID() );
	}

	foreach ( $secondaryQuery as $post )
	{
		var_dump( get_the_ID() );
	}

How can we mix together? For Instance. What if I want two different results mixed together forming one result that order-by "date" of each post?

I am not sure what you are up to. The WP.SE answer explains whats's happening here. If you got a different question, please ask a follow up question on WP.SE directly.