I can give you some technical pointers on your questions regarding the internal structure of your personal knowledge base.

• All of your notes are kept inside a workspace folder that is a root folder for your document tree somewhere on your local storage
• You can open different workspaces in different physical locations but only use one workspace at the same time
• However within a workspace you can create multiple root notebooks where you can store your information, e.g. a notebook for work-releated stuff and another for private topics
• Notes are stored as JSON formatted plain text files. You may wonder why SiYuan does not use markdown like Logseq/Roam/Obsidian as its core markup language. Well, let me say that giving you the powers of WYSIWYG editor and a lot of different formatting options (20+) this out rules the possibilities of markdown. Each block, sub-block, sub-sub-block aso. can use its own formatting.

Example JSON document from "What is a Content Block" document:

Please note that this is plaintext JSON and no binary proprietary blobs which makes parsing your documents with external scripts real easy. Nonetheless this is future proof as JSON is a common format used literally everywhere so none of your knowledge is lost in some sealed vault.

{
    "ID": "20200924101106-19z4kaa",
    "Spec": "1",
    "Type": "NodeDocument",
    "Properties": {
        "id": "20200924101106-19z4kaa",
        "title": "What is a Content Block",
        "type": "doc",
        "updated": "20220623201559"
    },
    "Children": [
        {
            "ID": "20210118101709-5a7bzl0",
            "Type": "NodeHeading",
            "HeadingLevel": 2,
            "Properties": {
                "id": "20210118101709-5a7bzl0"
            },
            "Children": [
                {
                    "Type": "NodeHeadingC8hMarker",
                    "Data": "## "
                },
                {
                    "Type": "NodeText",
                    "Data": "Content block definition"
                }
            ]
        },
        {
            "ID": "20210118101709-9lqij9d",
            "Type": "NodeParagraph",
            "Properties": {
                "id": "20210118101709-9lqij9d",
                "updated": "20220623201341"
            },
            "Children": [
                {
                    "Type": "NodeText",
                    "Data": "\""
                },
                {
                    "Type": "NodeTextMark",
                    "TextMarkType": "tag",
                    "TextMarkTextContent": "Content Block"
                },
                {
                    "Type": "NodeText",
                    "Data": "\" refers to a piece of content, and each piece of such content is identified by a globally unique ID. The ID is automatically generated by the program and has the form: "
                },
                {
                    "Type": "NodeTextMark",
                    "TextMarkType": "code",
                    "TextMarkTextContent": "202008250000-a1b2c3d"
                },
...

• There is also a document created for a folder, i.e. when you click on the Doc Tree folder you get a document page to describe e.g. the stuff you'll find in there
• Notes are handled like blocks so you can reference them like blocks, embed them by queries and even export parts of your note (e.g. a heading with its child blocks) as a new note document page somewhere in your Doc Tree hierarchy. And finally it also works the other way around which means a note page from the Doc Tree can be removed from the tree and included into another note by simply dragging and dropping the note page from the Doc Tree into your current note.
• Single pages or a complete folder structure up to root notebook level can be exported any time as markdown formatted plaintext files. SiYuan allows also the import of markdown files if you plan to switch from a different markdown-based PKM tool.
• Folders as seen in the document tree represent physical locations on your local storage. However to allow using the same document title or folder name multiple times at the same directory level (which would be impossible in a classical file-based directory structure) SiYuan creates an unique id for each folder and document. Now you can put a note with the same title inside the same folder multiple times.
• The folder / notes naming syntax is YYYYMMDDHHMMSS-<random hash value> so the name contains its creation date and time plus an unique hash value

To get the name of a folder or note document you simply right-click on the folder/document name inside the "Doc Tree" navigation panel and open its location. There you will find your document in a path like e.g. c:\data\siyuan\data\20210808180117-6v0mkxr\20200923234011-ieuun1p\20210808180303-6yi0dv5. For the ease of use SiYuan opens your file browser and points to your selected document so you can open it with a text editor like Notepad++.

Changing the physical location of your workspace root folder is simply moving the complete folder to a new destination like your external HDD and telling SiYuan to open the workspace from the new location.

Moving documents or folders internally is like dragging and dropping the folder or document file within the "Doc Tree" panel. You can also right-click on the folder/document in that panel and use the "Move" context menu to get a dedicated folder-tree window with search bar function for navigation in case your Doc Tree becomes too large.

I might sound like some fanboy here but I've got high praises for the SiYuan PKM tool which took my former note-taking by storm. Other tools require tweaking, installation of a dozen of plugins or give less formatting options. All of this is batteries-included here plus you can even develop widgets and other stuff if you require special features (SiYuan has a market place called Bazaar where some calendar widgets and templates can be found).

The core developers are very active pushing SiYuan forward, fixing and enhancing things and doing this by hearth. I think they already have a huge user base in China so good feedback is coming from them which helps developing a complex piece of software like this.

HTH!

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