You will need a multi-entry visa for Vietnam since Siem Reap is in another country (which also needs a visa).
I would suggest flying to Da Nang, first night in Da Nang. Drive up to Hue (disclaimer, I have not been to Hue) for the day, and have your driver return you to Hoi An. 2 nights Hoi An. If possible, be in Hoi An for full moon.