Proper Overrides and Such

This is an awesome project! If I can help in any way let me know.

I have a couple of questions.
Sorry, but I rarely use distributions to get started because they can be challenging to maintain.
So bear with me please.

What is the proper way to update modules in this distribution?
For instance, I see there are a few security updates. Should I wait for your next release?
"drush up" gets me the latest modules, but If you upgrade your profile, will I have issues?

Also from what theme should I create a basetheme? I have some changes I need to make to template.php

Lastly, If i have changes I want to make to your code where would you suggest I do that?
For instance I made one simple change to this code below (openlucius_core.module)

/**
 * Custom function to build a select from entity references.
 *
 * @param array[] $items
 *   The items to put into the select.
 * @param string $id
 *   The id to target, the select has nothing by itself.
 *
 * @return bool
 *   Build version of the select.
 */
function openlucius_core_reference_select($items, $id = "") {

  // Check if not empty.
  if (count($items) > 0) {

    // Create build for rendering.
    $build = array(
      '#type' => 'select',
      '#attributes' => array(
        'class' => array(
          'selectpicker',
        ),
        'data-live-search' => 'true',
        'data-width' => 'auto',
      ),
    );

    // Add id if not empty.
    if ($id != '') {
      $build['#attributes']['id'] = $id;
    }

    // Loop through items.
    foreach ($items as $item) {

      // Fetch title.
      $title = openlucius_core_fetch_node_title($item['nid']);

      if ($title) {
        // Build path.
        $path = url('node/' . $item['nid']);
        $options[$path] = $title;
      }
    }
    asort($options);
   //THIS IS MY EDIT >>> A SIMPLE CHANGE FROM GROUPS TO PROJECTS
    $options = array_merge(array(url('<front>') => t('Projects')), $options);

    // Add options.
    $build['#options'] = $options;

    return drupal_render($build);
  }

  return FALSE;
}