My husband and I decided to start our trip with the 3 night Siem Reap hotel package and then the 7 night cruise with a 2 night Saigon stay. Here's what I learned from taking this trip:
You do need to get visas for Vietnam ahead of time. You can do this through an agency or directly with the consulate. If you start in Hanoi, you need a multiple entry visa. If you start in Siem Reap like we did, a single entry visa is needed. You also need a visa for Cambodia but that can be bought at the airport. We did e-visas via the Internet. I had them within 24 hours. AMA also has an account with a visa agency and you can use that service if you wish.
Cambodia is very polluted. So if you have respiratory issues, make sure you have all of your medications. I have asthma so I had a breathing treatment before I went. The pollution still bothered me.