First off, even at it's close focusing distance of 1.5', that 50mm is only going to have a quarter inch (6mm) depth of field. At anything under 1', you will have nothing in focus.

Now, to explain why some things are in focus: It sounds like you are having issues focusing because of the focusing screen in your DSLR. Modern DSLRs have a focusing screen intended to brighten the image you are viewing with slower lenses most commonly used in conjunction with AF - nearly everyone uses a kit lens and AF never venturing into MF.

The downside of the focusing screen is that when you get a wide aperture and resulting shallow depth of field, you are actually seeing far more in focus through the viewfinder than is actually in focus on the sensor. This is far more problematic for you because you are left with f/1.8 at close distances where the depth of field is, for all intents and purposes, non-existent.

Also, it sounds like you are misunderstanding depth of field a little bit. You mention that the depth of field is too shallow, even for macro. As you get closer to your subject, depth of field decreases. For macro work, you actually want to stop down the aperture so you increase depth of field as much as you possibly can to keep your entire subject in focus.

Even if you did change the focusing screen to a split prism screen, which would accurately show you what is in focus at shallower depths of field, you are still going to have a massively frustrating time getting anything in focus with that lens stuck at f/1.8 at close distances.

Again -- Even at it's close focusing distance of 1.5', that 50mm is only going to have a quarter inch (6mm) depth of field. At anything under 1', you will have nothing in focus.