If you want to directly convert the statements into questions (in other words, you are not trying to pose questions which would cause the statements to be answers)
Is this your second stay here?
Is this the second time you have stayed here?
Is this the second lesson?
In other words, it is the very basic English manner of creating a question by reversing the order of the subject and verb. These all create yes/no answers.
But if you are trying to create questions which might cause someone to answer with the statements you cited, you do the following:
The idiom you would want is 'how many' in each case. It is an extremely common expression for asking about amounts. You would use 'how many' for countable items, and 'how much' for uncountable ones.
How many times have you stayed here?
How many times have you been here?
How many lessons have there been?