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I finally figured it out!!!

The "inspector" I needed to look into was the one named Magnets.
The boxes the I want to join together with a line snap to different parts of the next box according to where I drag the line.

The trick is to change the placement of the magnets, so the line doesn't "snap" to where you don't want them:

1) click once on the box you'll connect the line to
2) Go to "Inspectors" -"Magnets"

3) Change where the magnets are placed by selecting a different placement layout (the blue boxes on the right hand side).
For example, change to a setup with fewer magnets.
You may also manually add or remove magnets (use the + and - buttons) and manually move the magnets to where you want the line to "snap" to.

Other tricks for placing a line to a specific section of a box:
1) First join the boxes together. Don't mind where the line connects
2) click once on the line, selecting it
3) now click and drag on the green dot at the end of the line (or red dot at the start of the line) and drag it to where you want. You can "snap" it to the closest magnet.

If you want to connect the line anywhere to a box:
1) turn off the magnets (remove the tick next to "Enable connections"
2) The line will no longer "snap" to specific parts of the box
It will however "snap" at specific intervals because of the grid, making it easy to make a neat, aligned connection.
3) If you want to place the line absolutely anywhere you want, be sure to turn off the "snap to grid" function as well ("Inspectors"-"Grid").

Anyone got anything else to add?
Hopefully others reading this won't struggle as long as I have.