Hi Gary,
Thanks for choosing Meta Box!
In Meta Box, code that you're using in your PHP files and the field groups you created in the Meta Box Builder work independently and simultaneously. There's no connection between the code and the fields created in Meta Box Builder.
Unless you export the code from the Meta Box Builder and put it in your theme/plugin. In that case, what loads first will take effect. But you should avoid this as it's confusing. If you want to use code, you should move the field group in Meta Box Builder to Trash (or switch to Draft) to prevent it from loading.
Besides, in Meta Box Builder, the custom attributes feature is powerful enough for you to add custom settings for the meta box or for the fields. Using this feature will help you achieve the same effect as using code. However, if you want to use code, please just use it.