If I have to extract a bunch of mesh folders into the data files folders... what do I do if there is already a folder named "A" when the one Im extracting is A also?

Do I just keep making subfolders within the mesh folder?

If you extract folder "A" where another folder "A" exists, you should be giving the option to merge the two.
When they ask you if you want to overwrite, they mean 'merge the 2 folders' not 'crush and erase the previous folder'.

Yup

so I take it I should merge them?

yes/no/maybe? I am a noob and keen to install bloodmoon for the extra landmass.

Merge them, yes.