It really depends upon the design of the touch hole and its location...
With that type, you don't want to fill the pan...

Both of my flinters have touch holes coned from the inside and the touch hole is higher than the one in the pic...Mine are behind the frizzen when closed, in this situation it is OK to fill the pan as the touch hole can't become plugged with the prime...

One other point....Flintlocks can go off even when there is NO prime in the pan, trust me on this, I've had it happen!!! When you have one of those situations where the first shot doesn't go off and have to stop and knap the frizzen, don't check your sparking with a load in the barrel!!! It's safer to knap with a small brass knapper or change out the flint and unload...I always keep a freshly knapped flint in my patch box, so I don't have to leave the gun loaded and go find one...If you have to knap without a brass knapper, put a round toothpick in the touch hole (or a small feather) to keep sparks away from the main charge...

While I'm on this...If you do have to pull a load, first pour water, oil, solvent down the barrel to wet the main charge...Be Safe, these things are dangerous and require a little more thought than a cartridge gun...