I used the standard antenna resting on the Velux window itself - stuck the the metal "CD" groundplane and fed out of the vent at the top of the window (be careful not to cut the cable with the latching mechanism). I did get a slight bias in the direction the antenna faced, but it wasn't a major problem.
Make sure you leave plenty of time for the polar diagram to build up, and remember that if there are no aircraft in a particular part of the sky (no air routes) then that will affect your polar diagram. Height is everything, so if you can get the antenna even 6 inches higher, you will get a better performance.
You could try the antenna in the loft, but I would always try to get it outside. Half the fun is trying different locations :-)
I now use the BS1100 external antenna.