I am no expert in the matter but here is what I believe the reason is from listening to Sean Spicer in his press briefings.
Phase 1. Is to pass the Health Plan under budget reconciliation which means those things that effect the budget. This only requires 51 votes.
Phase 2. Is where Secretary Price can go and get rid of or make changes to ALL the rules and regulations that Kathleen Sibelius had control over. She made a gazillion rules and regs.
Phase 3. Allowing insurance across state lines. Medical Malpractice Reform. Associated Health Plans or high risk pools ect.
I am guessing because these would be new laws it requires 60 votes. So this is why it has to be done in 3 stages.