Say there is a competition day after tomorrow, and you are learning guitar to compete there. You are yet just a novice. Your teacher might ensure you by saying,
You will definitely learn how to play the guitar in time.
in time would describe the idea you will learn to play the guitar fluently and flamboyantly just in time for the competition, like during the last-minute rehearsals.
Now, if you are learning it without the hindrance of a competition coming up mid-way, you may take months to learn the same thing. In that case, both the above sentences would make sense.
You will definitely learn how to play the guitar with time.
You will definitely learn how to play the guitar over time.
with time and over time mean essentially the same thing, as time passes by. However the use of 'learn over time' is far more common than 'learn with time', at least according to this Google Ngram.