As I understand it, flyspell is a secondary on-the-fly mode that emphasizes spelling errors. It uses ispell (or what you set as ispell-program-name) to do the actual spelling.
flyspell, . .
, ? ( , , ispell? Aspell?)
? ,
(setq ispell-personal-dictionary "my-personal-dict")
. emacs. ( C-h v ispell-personal-dictionary) , . , - , , , , , , , .