The Capital letters are the lower pitched, bass strings and the Lower-Case letters are the higher strings.
So your bottom C is a single string, and the others are tuned as matched pairs, with your top four strings (A d g c) as fourths. I would start with your A, then tune your F and C downwards from there, and then work upwards tuning your higher strings. It doesn't really matter, but if you are having trouble this should make it easier as you should be able to tune fourths without the tuner.
Regarding the 440 - that is the most common standard for A to be tuned to. So if your tuner is set to 440Hz I'd recommend leaving it there.
Just to consolidate a couple of the comments:
Daviderath.com has somestraightforward guidance on tuning notation, and Oudcafe has guidance on tuning and on stringing your Oud, including this handy picture: