There was a long discussion about this over on the Moyer Marine forums a while ago. I also run my blower while the engine is running -- anything that helps get the old girl some cool fresh air while she's working is a good thing in my book.
I also run it for several minutes after I shut her down, just to blow more of the hot air out of the engine compartment. Keeps below decks cooler, too.
S/V Free Spirit
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