Choose Files button confusing

Yes, it can be done. You need to:
1) Activate option “Check it to disable automatic show file upload field” in plugin settings. (menu Settings -> Comment Images Reloaded).
2) Add in necessary place on of snippets:
– If there is function call comment_form() in comment.php of active theme, then it is necessary to pass parameter, like this

$args = array(); //empty array or value of your theme
if ( function_exists("get_cir_upload_field") ) {
    $args['comment_notes_after'] = get_cir_upload_field();
}
 comment_form( $args );

– If there is no call comment_form(), find closing tag </form> and button of sending comment and add code before them:
<?php if (function_exists("the_cir_upload_field")) { the_cir_upload_field(); } ?>