Loading specific products
I haven't tried Commerce myself but I think something like this should work:

{% set products = craft.commerce.products.type(yourType) %}

//make an empty array
{% set filteredProducts = [] %}

{% for entry in products %}
    //check for your conditions
    {% if (entry.checkboxFieldhandle) or (entry.hasStock) %}
        //add each entry to your products array
        {% set filteredProducts = filteredProducts|merge([entry]) %}
    {% endif %}
{% endfor %}