AstroDude42
Hi - Thank you very much for you reply, the Darks aren't so much an issue, it was just that I shot two targets one night using different filters, and then when I did the subsequent flats and dark flats they all ended up in the folder together - I figured that If I typed a name in the box that would somehow end up distinguishing the two sequences (with different filters) apart, however they all ended up lumped together in one folder and all had exactly the same name.
I will look in the main camera settings as you suggested, and thank you again for taking the time to give such a detailed explanation, very helpful.
Regards
Andy H