the answer to your question is yes,
usually.
In the best of all worlds, your touch hole will be in the "sunset position," that is, just level with the upper edge of the pan, so if you drew a line on the barrel from the front to the back of the pan, the hole would be right on it, or very slightly above - think six o'clock hold. Ideally, the hole would be evenly centered between the front and back edge of the pan.
we do not, to the best of my knowledge and belief, live in the best of worlds. your touch hole may be in the 'sunset position,' or it might not. this doesn't mean that your gun is no good- far from it- your hole may be out of position and the gun might still function perfectly well.
what i would recommend that you do is to tinker with your loading set up. i had been told for years to fill up the pan or the gun would never shoot - it was only until i was encouraged to try something different that i came to realise how quickly a flintlock can fire. in this light, i encourage you to do the same. start by filling the pan so that the level of the powder is well below the touch hole, then increase or decrease the amount of primer used, and try banking the prime away from the hole, and toward the hole, or level in the pan. it should go without saying, but only change one variable at a time, and take careful notes of what you're doing so that you can repeat success and not do a do-over on failed tests. eventually, you will come upon a depth and orientation of powder which works best for that particular gun.
here's the bad news: you will have found a depth and orientation which works best for that particular gun. the next gun will most probably want to be primed in an altogether different configuration.
part of the charm of flintlocks (to my mind) is their feisty and individualistic natures. the upside is that once you get it working well, the success is all the sweeter.
to maximise the potential accuracy of your rifle, i would recommend Dutch Schoultz' method. If you do what he says, your groups will shrink. His work is the best non- shooting accessory i have ever purchased. Here's a link:
http://www.blackpowderrifleaccuracy.com/
good luck with your project!
Make Good Smoke