Don't be sorry about asking questions as long as you have read the docs that are available and the ones that come with the game, and even after that you are left with doubts, its always a good idea to ask.
The aircraft collision happens because you are not following the directions given by the ATC, I.E if it tells you to descend to x y z, do so. if it tells you to climb up to x y z height, do so.
Always make sure your frequency and transponder codes are up to date. if you press f and it just says a number without a prefix of new then the frequency is up to date. if you press space and here no code such as scquock 4 2 3 4 whatever the numbers,then your transponder is up to date,too.
If you are still facing the collision issue after you have made sure of all this,then your ATC files are probably screwed up. just get the latest from the website.
If that doesn't help, write back on here and we can come up with new suggestions for you to try
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