Some folders may be treated specially by the system - like "Documents" or "Desktop" or "Music".
I don't recommend that you delete them (and I think you actually can't).
But let's take as an example the "Documents" folder, and suppose you want its contents to live in your external drive.
Step by step:
1) Create a new folder in the external - let's call it "My Documents" (but you can call it anything really).
2) Drag all the the contents of "Documents" to "My Documents". This will COPY them, and may take a while, depending on how much content there is.
3) Drag all the contents of "Documents" to the trash (since you already have copied them elsewhere and want to reclaim space). Empty the trash
4) Command-Option-drag "My Documents" to your home folder.
Now you will have "My Documents" sitting inside the home folder, but it is actually just an alias to the real folder in the external. For practical purposes, though, it is pretty much as if it sat right there inside home.