Hi Tarjam!
In many cases the use of a preposition really depends on the context. For example:
The verb: La'avore (לעבור) - Can be used in a sentence with the preposition - על, מתחת, אל, מ
To go over a text - לעבור על טקסט
to go under the bridge - לעבור מתחת לגשר
to move to a new apartment - לעבור אל/לדירה חדשה
So, as you see, there are many options. I suggest that every time you see a sentence with a preposition, try taking it and make up a new one, Maybe it'll help.
Aviel