Well if you just take a look at where ACF saves the image field for the optionspage you should be able to do a set_option or add_post_meta depending on if it’s in wp_postmeta or wp_options..
However a different solution you could do is to have an if statement around the output of the logo (this assumes that the return is set to image URL):
<?php
if(get_field('custom_logo_field', 'options')){
$image = get_field('custom_logo_field', 'options');
}else{
$image = get_bloginfo('template_directory') . 'images/default-logo.png';
}
?>
<img src="<?php $image; ?>" alt="company name" id="logo" />
