What matters is not what you read but how you read it.
Literal
Problem [copula-な] [nom-の] [topic-は] what [obj-を] read [Q-か] [not-ではなくて] how read [Q-か] [copula-である].
Pairs two embedded wh-questions in a contrastive structure — 何を読むか ('what to read') is negated with ではなくて, then どう読むか ('how to read') is affirmed. A quotable, elegantly parallel construction.