Let me try to give a small crash course.
For a tune to be in tune, all notes need to belong to the same scale.
To achieve this, you either need a very well musical hearing (which most people who start making music don't have)
Or use some tools which are in lmms.
In the piano roll you can pick the scale, major or minor for example but there are more.
After you picked one, move you're mouse over the keyboard in the piano roll, right click and select mark current scale.
Now all you have to do is only put notes on the blue lines. (not on the black lines)
What you can do with the tracks you already made is to find a scale that fits most notes.
Then you will see a few notes not on a blue line, move those notes to a blue line ( so up or down, its you're choice)
The box in the below picture, which says no scale. If you click it, you can pick a scale.
This should together with the vids from musicbear get you going.
Hope this helps.
. But you do need your ears to get accustomed to this.