Whenever, I try to make a link to another note within a table it gets mixed up thinking part of the table is a part of the link. How can I fix this? I’m sorry if I mix up terms, I am still figuring things out.
You’re trying to use [[NoteName|Alias text]] within a table, and that does indeed get you into troubles since the | is used a table cell delimiter. To avoid this you need to change the format of the links used within the table.
So try doing [Alias text](NoteName), or if the note name has spaces try doing [Watch & Learn](<How-to (Top-Down Thinking)>) or similar. Note the angular brackets around the note name in that last case.
Also note how the alias and note name switches place in the various link formats. The former is called wikilink syntax, and the latter markdown links. If you want to switch to always using markdown links, you can go to Settings > Files & Links > Use [[Wikilinks]], and disable it. I think, you’ll still be able to use [[... for auto completion, but I’m using Wikilinks most of the time myself.