Yes, you can adjust any one of the settings independently of each other in Manual. That's why we love Manual.
Having the little line in the middle is what the camera's auto-exposure system thinks is right. Sometimes it's wrong. Scenes that are mostly black or mostly white will be metered incorrectly this way. The autoexposure system is metering and finding a median value, which it then decides is going to be the middle gray value, exposure-wise, and determines your settings based on that.
But if you're shooting a snow scene, and your scene is mostly white, a value of white or very light grey is going to be set to be "middle" gray, and as a result, your shot will be underexposed. If you're shooting a panther in a coal mine, a value of black or very dark grey will be set to "middle" gray, and as a result, your shot will be overexposed.
This why we like Manual mode and exposure compensation.
As for the histogram, don't make the mistake of believing that there's one specific way the histogram
should look. All the histogram is doing is describing what's in the frame. You're mostly concerned not with if lines are there, or how high they go, but whether or not you think you're missing information off the ends of the scale, or where specific bumps are placed, depending on what you think the scene should be exposed for (subject, background, etc.)
This article is probably the best one I've seen on what histograms are and how to use them:
Understanding Histograms