How to properly connect PLL in Cyclone V?

First and foremost, you need to do it in a way that works. You've clearly thought about the solution, it's very considered and thorough. Yes, synchronising signals and persisting them - especially when they take time to settle - is essential. There are plenty of ways to do this but they'll all fundamentally rely on counters. Providing you've the space in your device to do all this then fine (I don't see 'all this' being particularly big).