Best way to transfer and organize iTunes library

I am moving from a Macbook Pro to a Mac Pro. On my Macbook Pro, I recently realized that I had been manually organizing music in folders, and then adding them to iTunes (dragging and dropping), which would copy them to the iTunes folder. A bit redundant.
On my Mac Pro, I have a specific HDD that I would like to use for iTunes. I have the iTunes folder from my Macbook Pro, as well as another iTunes folder from a different computer. Both have folders have been organized by iTunes, but I am not sure how best to combine them for the sake of neatness.
I just went into iTunes preferences and changed the media folder location. Should I also check the "copy files to iTunes Media folder when adding to library" box?
How do I have everything stored on the specified HDD in a single, organized folder, without it copying everything to an iTunes folder in my home folder?

bump. Anyone know?

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