1. Use AHCI for the "On Chip SATA Device". You always want AHCI enabled. As for the "On-board PCI Device Storage Controller", which is the JMicron controller, you should keep that as AHCI as well unless you don't have any devices connected to its ports, in which case you should disable it.

2. Other than enabling AHCI, nope.

3. Yes, leave all memory in place, it will be fine.

Be sure the auxiliary Molex plug on the motherboard is plugged in should the motherboard require extra power.