I'm starting to shoot more and more in manual, so making sure the 'line is in the middle' depending what aperture I shoot at. It's just knowing where to meter/focus that's the thing I'm going to start looking into
If all you are doing is chasing the meter needle back to the middle then you may as well stick with autoexposure, as it can do the job of adjusting values far quicker than you can. The main advantage of shooting with a manual exposure is so that once you have established an exposure setting that is correct for the incident/ambient light upon the subject and scene it then remains locked and will not waver from the values you chose. It is like having an infinite exposure lock, changing only when you want it to. There is nothing at all to suggest that you should be aiming to centre the needle when shooting manual. You should be aiming to get the needle positioned to just exactly where it should be, which might be in the middle if you are metering from a perfect mid tone such as a grey card, but could just as easily be something completely different. I will commonly meter from my own outstretched palm at + 1.3 stops and fix an exposure manually at that setting. Unless the light changes then that's me done. No more worrying about what the camera's meter is picking up, or what metering mode I'm in, or how much EC to dial in. The meter can bob about all it likes, and the beauty of shooting manual is that I don't care.
In contrast, using autoexposure, the camera is going to repeatedly re-meter the subject/scene each and every time you half press the shutter button, probably changing exposure values depending upon just how you frame the subject/scene and just what the subject is. That can be very tedious to deal with. You might have an AE lock button, but the lock only lasts a few seconds, and then you have to start again.
Take a look at the two examples below. These were shot with a manual exposure that was identical for both. If I had chosen to use autoexposure I think there is a very good chance that the camera would have decided the white car was too light, thus reducing the exposure, and the black car was too dark, thus increasing the exposure. In both cases the camera would have been wrong, unless I was riding the exposure compensation dial like a twirling Dervish and getting lucky with each and every guess at how much EC to dial in. By shooting in manual mode I was able to set an exposure that was suited to the LIGHT (a grey day, just about to rain, no changes in light levels expected for many minutes to come) and did not care two hoots about the tone of my subject, and was not in any way thrown off by it.
A similar example, this time in bright sunshine. My exposure here is actually 1/3 stop brighter than "Sunny 16" and there was a little recoverable clipping on the white car, so I just pulled the exposure down by 1/3 in post. By exerting manual control over my exposures there was never any danger of the metering getting all confused and throwing me a curved ball....
Another advantage of shooting manual, if your meter and EC capability only goes to +/- 2 stops, is that you can indeed meter and set an exposure that places the highlights right at the clipping point, which is +3 stops in all six of my Canon bodies.
I'm quite surprised to discover that Nikons don't lilke taking the exposure that far, but it's no biggy - just work to the limits of your own equipment. The important thing is to know what those limits are. By the way, it is neither good, nor bad, if Nikons can't be taken to +3. It's simply that the metering is set up differently. Or, it might be that the software used to process the files is working in a different way from Lightroom, or an unusually aggressive tone curve is in use. If shooting to JPEG then I accept that taking highlights to +3 might be just a tad too far, but certainly it's no problem when shooting raw with my Canons.
