Unfortunately I found the siphon an incredible pain to start without the pump. You have to put a bit of airline tube up the siphon to the same place and then suck out the air by some other means, usually by mouth. I got fed up with that quite fast, particularly since I could never seem to get all the air out that way...some would always sneak back in as I was trying to either cap off the airline or remove it.
The siphon tube can be lifted (you can also lower the black box inside the tank, which lowers the waterline; same effect as far as distance the water is traveling), but it slows the flow a slightly the bigger the gap is between the waterline and the bend in the tube. If it only needs to be lifted a little though, I don't think you'd see much difference, particularly if the waterline was high.