Hi. I just got my first hip flask today in the mail. I got one because it’s Halloween weekend and I’m going to be traveling a lot and I didn’t want to bring massive bottles with me. They don’t really sell stuff like that around me as I’m very rural and no one really drinks. It came with a funnel to make it “easier” to put the alcohol into the flask. Every time I tried to fill the flask, the funnel came filling up and wouldn’t go down until I picked it up slightly. I eventually managed to do that but it took ages as the flask is around 180ml and at most I could only get not even a quarter of a shot glass in at a time. It made the flask, the table, me, my bed, everything wet with alcohol. I thought they were meant to be discrete? I probably did do something wrong but I don’t know what as this is my very first hip flask as a young woman. I’m not sure if the flask is leaking or not? The rim is still kind of wet from the alcohol and I don’t know if it’s leaking or not which would be awful because I mostly got it to travel with and it was a bit expensive than the others I saw. How can I tell if it’s actually leaking?
I think you need to pour slowly or as you said, raise the funnel slightly, as you need an outlet for the air as you replace it with water! Hope that helps! That’s how i fill mine! 
P.S. when i said water, i meant alcohol! 
I will add that it’s not the size, as i had to use the same method topping up the windscreen washer reservoir on Tuesday!
As Will said hold the funnel slightly above the the opening and fill with the other hand. You want the stem of the funnel to be in but the wide part slightly above the flash opening to allow air out. It will always be slow to fill due due to the size of the openings but that helps you not overflow. An alternative if you are just wanting smaller bottles to carry around just wash some smaller bottles and use them, used to do this when going to camping music festivals as glass is usually barred so filled old coke and irn bru bottles with vodka.
if its to discretely take alcohol in somewhere then thats a different ball game. During my uni sports ball days the favourites were to use resealable caprisun packets and tape them around the inside of legs or stomach.
They are tough as you can’t see how full it is getting. The idea is to let it breathe while you pour it in. Just pinch it at the neck and don’t let it rest on the opening and you will likely still overflow.
However, rest it on a small plate and then when it overflows just pour the amount into your mouth or back into the bottle.
It isn’t a great setup usually.
If the funnel is filling the opening of the flask, the air from the flask has to come back up the funnel when you displace it with booze. The ideal is if the funnel is slightly smaller than the opening of the flask, so the air can escape round the side.
I have large 50ml syringes, and measuring cups for cocktail mixology, and these are perfect for filling mine, and knowing how much I’m putting in. 
I would decant the liquid into a pouring jug and then use that. Easier to control the flow and watch the sweet sweet nectar flow into the flask.
Raise funnel to allow air to escape from the flask as you fill.
Pre measure 180ml before you pour so you get he exact right amount in with no spillage.