Multiple content types in a library causes metadata problems on upload

MarBisso you've started adding all your custom metadata columns to both your Document Set content types. Ultimately however you are adding Documents (items with Content Type "Document") to your document set. Documents have their own content type (Document instead of Document Set) which will need your columns too. Hence, adding your metadata columns to the Document content type made the columns appear in your forms. 

Basically you'll need to define another 2 different Content Types based on "Document" to get the behavior you want (e.g. "Engineering Document" and "Energy Services Document"). You can then add the columns required for each type of document to the Content Type. Next, you'd probably want to configure Document Set Settings to allow only the matching Document Content Type. Your Document Library should be configured with the 4 Content Types you end up with:

1. Engineering Document Set
2. Engineering Document
3. Energy Services Document Set
4. Energy Services Document

Hope this helps!