Hold everything, folks. Raising the stem changes the angle of your arms to your body but otherwise changes very little unless you make a big change. A 1" rise brings it .3 inches closer to the saddle. You need to determine if the distance from saddle to bars is correct, which means first setting saddle fore-aft position correct then going to a different stem length if necessary.

As pointed out above a too-small bike is very possibly the problem. In that case a higher stem will have you putting a lot of pressure on the saddle and you will be back asking how to solve that problem. If you can't post a pic then tell us your inseam (jeans length) and distance from crank axle center to top of seat post