During vis-mig stakeouts, I leave it running, and start a new file every 30 minutes or so. I've found that there is often too much going on already, and the seemingly simple task of hitting the record button is too much of a distraction. If something good goes over, I make a note of the time on the recording display and cut the section out when I get home.
To combat the wind, I try and put the recorder either in a dip, or surround it with a scarf or towel shielding it from the wind.
Peter