So I have just begun using a metronome and I had a question. I've been practicing the aeolian mode at the 12th fret. Now I understand that the basic premise of playing one note per click. My question is if I'm hitting my notes on the 3 clicks I'm hitting them on what do I do with the 4th beat or does it matter?
So first of all, the correct name for the scale you're playing is E minor, if your guitar is in standard tuning and you're starting on the low E string.

And how much do you know about rhythm-related music theory? Because you seem to lack some basic understanding here. Metronome is supposed to keep time, or indicate tempo, however you want to look at it, you can think of it as a drum beat. So, if you're playing a song in 4/4, and you're playing one note per click, you're playing quarter notes, if you play two notes per click you're playing eighth notes, if you play three notes per click you're playing eighth note triplets etc etc. so if you play the E minor scale with just quarter notes, you should land on the note "A" on the fourth click, or fret 12 of the A string.

Now I'm not sure if I even understood what you're asking, but in any case the metronome is there just to help you play evenly in time. Maybe you can try to explain in a little more depth what exactly is your problem here?
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I realized my original post may have been quite confusing. Anyway I recorded myself practicing around 100 bpm does this sound about right?
It sounds like a pretty good start, but i would recommend taking 3 notes out of that scale, and play them over and over in a loop. And just focus on really nailing the click every time. Your timing is alright, but it ahead of the beat a little bit towards the middle of that clip. If you listen back can you hear how the note is coming before the click?

The other thing is, you are biting off more than you can chew by practising the whole scale all the way through every time. Your hands won't really LEARN anything that way, because there is too much information coming at them. Take 3 notes and practise them over and over for a long time  - like 10 minutes. It is supposed to become like a meditation. You bring things into your awareness - the sound of your note in relation to the sound of the click, your hand positions, how your hands feel, the Movements you make with your hands. Metronome practise is a way to really bring all of those things under the microscope so you can see what is going on. Then you can focus on the sound of the notes, also, make sure they are all equal in volume, all sound even, all have the same picking sound, etc, etc. You will discover a million things eventually.

But just start with a short loop of 3 notes, and really pay attention - every note ask "How close is that one to the click?" Just 10 minutes at a time, also. No more. Unless you are really on a roll, leave it after 10 mintues or you will stress yourself out. I can hear it in your playing - you will stress yourself out.
Last edited by ben_mann at May 27, 2017,
I've made a video lesson for you. It started off with just a demonstration of metronome practise but it turned into a fully fledged lesson so watch it through past the first bit minutes of mostly practising. Don't skip because you might miss something important, and more importantly it sets the atmosphere as well.