Ben -
You can only have one functions.php per theme. But inside the Acamas functions.php you can include or require another php file. The best place to save your custom functions file ,so that it won't get overwritten or throw an error in wp-admin as a broken theme, would be in the wp-content directory. So you could add this to your Acamas functions.php.
require_once(STYLESHEETPATH . '../../../lib/my-acamas-functions/my-functions.php');
Then make a folder in the wp-content directory named my-acamas-functions and save all your functions to a file named my-functions.php. Find out more about require_once
-Gene