In the example I often remember the boy [that I went to school with [when we lived in India]], the main clause of the relative clause is I often remember the boy, while the main clause of when we lived in India is that I went to school with.
'Main clause' is not a very interesting concept for syntacticians, because main clauses are not clauses, just clause remainders. But it is sometimes useful for reference, i.e. when one talks about the relation between an element in a subordinate clause and elements in the main clause.
Sometimes main clause is understood in the sense of nonsubordinate clause or independent clause, as 'a clause that can stand on its own'. Note that this is very different from the definition given above. These two senses of the term are often confused.