Prepositions like 'in' ,'on', 'at' are both prepositions of place and time. They indicate the position of objects 'in the room' ( referring to being inside and within a place ), 'on the table' (referring to a higher position, at the upper surface of an object )and 'at the desk' (towards or in the direction of a certain object ). It is easy to understand them when they refer to places, the meanings are distinct enough to differentiate which one to use and there is no confusion. You are then confused when they are used as time prepositions as in ' on time' ,'on Thursday' , 'in the year','at noon'. You might ask yourself why not 'at Thursday' ,'at the year' 'in noon' ?? When using time prepositions such as 'before' and 'after' you will find it easy to distinguish,which to choose in a certain context, something either happens before or after in a subsequent order that will be clear from the context. In the case of those prepositions in particular ,you will surely get confused ,because it doesn't seem to follow a certain pattern or have a precise meaning .Fortunately there is a way to lessen this confusion: - There are some rules to follow there. 'in' is used for example for years, months ,while 'on' is used for days and 'at' for a precise time. You can check those rules here: http://www.englishclub.com/grammar/prepositions-at-in-on-time.htm - By practicing a lot through reading and speaking you will grow familiar with their correct usage and will be able to use the right one automatically. However there is still another confusing element, they are also used abstractly to indicate states ' in your mind','on a journey' ,'at ease' and many times used idiomatically as part of an expression ' in doubt' ,'at hand' ,it is on me'. Here again it is a matter of increasing the rate of learning idiomatic expressions and vocabulary in general. It is a gradual process and you won't be able to memorize them all at once. I hope this helps you figure out how to lessen your confusion about the usage of those prepositions in particular and the same goes for the other.

Inagine you have a box. the box is lying so that the opening is facing you. if you are to take a pencil and place it ON the box, it will go on TOP of the box. that is the surface it is ON. If you are to place the pencil IN the box, you place it INSIDE. The box, when the pencil is in it, is surrounding the pencil. If the pencil is AT the box, it implies location. The pencil was somewhere else and now is near the box.