I normally use cheap, lightweight water bottles to carry my water when I'm hiking. However, sometimes I'm with people who use bladders such as a CamelBak, and I offer to go and fill water bottles, so I have to fill theirs. Maybe I just need to ask them to explain or demonstrate the technique for me, but I find it really slow and difficult to fill those things, especially when I'm filling from a lake or pond. Is there a trick? If I stick the bladder under the surface, it sort of crumples, and when I pull it back up, it's only about 10% full. The best method I've improvised so far is to fill one of my own rigid bottles with water, then pour that into the bladder.
The answer depends a lot on the style of bladder, there are a couple different styles.
I have a classic camelbak, which has a nalgene sized opening on it and a handle to hang onto for filling one handed, so it's real quick and easy to stick in the water and fill up:
I've had other types of water bladders though that you had to fold the tops over and slide on a top piece. These types of closures are not as user friendly, but apparently leak less, and are able to hold back a lot of pressure which is why they're used on the fancy Geigerigs:
These ones aren't super easy to fill in flowing water, you need to use two hands and depending on the flow they tend to spill a lot. Easiest thing is exactly what you were doing, fill a bottle and pour it into the bag, I always carry an extra nalgene, even when I'm carrying my camelbak, it's handy to have for those small streams where you can't seem to get your bladder under the water.
Personally, I prefer the Camelbak twist closure over the slide tops, even though it can be a pain to open if you tighten it too much, and it does drip a bit sometimes, they're just easier to fill.
My standard daypack came with a Camelbak shutoff valve and quick disconnect for the bite valve. I upgraded all my other packs to have the same using Camelbak's HydroLink Filter Adapter kit, which also comes with an endpiece you can put onto a filter hose.
This allows me to stop for water and, without removing the bladder from my pack, simply disconnect the bite valve, plug my filter into the place where it was, and pump water through the hose into the bladder. I use this with both my Katadyn Hiker PRO pump filter and my Sawyer Mini filter and it works great with both. On the Katadyn, it takes about 40 pumps to add 1 liter to the bladder.