I go separate bags.
If your camera bag fits two AD360s and all it takes to keep them powered, then you must have a very large empty bag when you aren't bringing them!
Plus IMHO it gets confusing digging in one bag for flash accessorizes and having to push memory cards and lenses out of the way.
There are kits that are one bag, certainly. I just cant see a convenient one bag kit that includes a pair of AD360. 
For lighting in particular, I also really like to have that kit always packed and essentially ready to go, it is also storage. So it needs it's own bag. then it's a matter of which or how many bags I need to take ,. not always repacking with different stuff.