Some folks who are used to derailer bikes find wheel installation frustrating, especially with a nutted hub. This is usually because they don't know the technique of "walking" the wheel back and forth in the fork ends.

Start by installing the wheel at approximately the correct position and tightening the axle nuts. They don't need to be super tight at this stage, but should more than finger tight. Check the chain tension and wheel alignment.

Most likely, the chain will be a bit loose, but perhaps the wheel is correctly aligned. Loosen one of the axle nuts and push the tire to the side so that the loose side of the axle moves to the rear, then tighten the axle nut you loosened.

Now the chain tension should be better, but the wheel is no longer centered between the chainstays. Loosen the other axle nut and re-center the wheel in the frame. This will actually tighten the chain a little bit more.

The key is to keep one or the other of the axle nuts tight at all times, and "walk" the wheel forward and back.

This takes a bit of practice and getting used to how much axle movement is needed to adjust a given amount of chain droop, but it isn't really hard as long as you keep one side secured at all times.

[I like to leave the right-side axle nut a bit loose, get the chain a bit too tight, and tap the chain with the wrench as Sheldon describes for centering chainwheels. This way, I can move the rear wheel forward just the tiny bit needed to make the chain run smoothly. The wheel will then be skewed, and I need to readjust the left end of the axle, but this has little effect on the chain. -- John Allen]

Note, this technique doesn't work with a quick release hub, but those are generally easier anyway.