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I take mine during the imaging session normally. That is assuming that I'm not pushed for time or cloud moving in. Otherwise I do them while I'm packing up if the temperature was relatively stable.
I then set up a filing system for each object and method used to image with the top folder being the date eg 2007-10-24 then M31_135mm_600sec_ISO400, then in that folder I have one for Lights, ond one for darks. For Flats I use a single folder under the date folder at the same level as the object folder. I do this as I don't normally alter the orientation of my camera once I've started a nights imaging. If I do then I might place individual Flat folders in each object folder.
I find this is the simplest way for me to keep track of the images. Once I've processed each object in IP and have Fits masters and Tiff masters I will go through and delete the intermediate fits files that IP generates, just to keep free some space. A big imaging session can generate a lot of MB.
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