@bluewings666, if you search these forums, you will find numerous discussions of note-taking strategies with DTTG that may help you.
As korm points out, there are many choices for note-taking apps. Most differ just enough in features and function to satisfy some users and not others. In my exploration, the apps which integrate most easily with DTTG are the plain-text and Markdown editors. It sounds like you prefer note-taking apps that enable rich text, handwriting, and drawing. It is not difficult to store a copy of these types of documents in DTTG as PDFs and RTFs. However, editing the documents once they are in DTTG is more complicated and may be impractical for some users. You might want to consider leaving your rich text documents in their native form/app until you export them as PDFs or RTFs to DTTG for archiving along with related materials.
I am currently experimenting with using Agenda as my project note-taker. Some advantages for me are that it has one more level of organization than Apple Notes, and it easily exports notes in Markdown format, which is reasonably well supported in DTTG. For you, the current lack of Apple Pencil support might be a deal-breaker. But, I still exclusively create and edit the project notes in Agenda, exporting to DTTG as Markdown only after the project is closed. I use Apple Notes for all other note-taking, because most of it does not end up in DTTG. If it becomes necessary, I can export notes as either PDFs or RTFs, depending on the contents. They display well in DTTG to suit me.
If you manage to work this out to your satisfaction, please share the details with the rest of us!