There is generally a certain spot that sounds best to your ears. Try moving the pickup to a variety of locations, and listening to how the sound changes in each spot. Some will be brighter, some more mellow. Set the amp completely flat, and find the spot that sounds best. "Flat" means with no bass, mid or treble controls boosted from their zero position. Then try changing the amp settings and see what sounds best. When you identify the sweet spot for the pickup, measure it from a couple of reference points and mark it down. When you find the amp settings you like, mark those down, too. Keep this in your case, and when you go to play, you can start with these settings. You may need to adjust the amp to suit the location, but it should get you in the ballpark for starters. A standard dulcimer has only one bass string, and it's on the high end of the bass register at that. This dictates that it produces a somewhat bright sound. Locating the pickup on the melody side of the top will magnify this treble, while a spot on the bass side will emphasize lower sounds. Toward the bridge will be brighter also, and toward the nut is a little deeper. If you go too far away from the treble, the melody might not stand out enough against the drones or chords. Have fun learning what location does to your sound, the putty lasts a long time, and is cheap to replace. If you play a baritone or bass dulcimer, there will be a lot more low end to the sound, and you most likely would prefer a different location. Even in the same register, each dulcimer will have the sweet spot in a different location, so experiment with each one you plan to use the pickup on.
Paul