Yes, both plugins can co-exist without problems.
You can use Meta Box Lite to create more fields for your website. Removing existing fields requires investigating on how the theme author used Meta Box to create them. If he/she used code to create custom fields, then it’s required to use code to remove them. In any case, removing fields from the theme might break the theme (because the theme uses them somehow). It’s best to contact the theme author to get support for removing/changing those fields.