Siem Reap is belong to Cambodia not Vietnam. So you may need a multiple entry visa.
The fee for multiple entry visa ($50) is double that of single entry visa ($25), so I suggest you contact some of visa agencies for better advise. You may read the topic
http://www.flyertalk.com/forum/asia/...ietnam-50.html for visa agencies information. I personally suggest
http://voavietnam.net and
www.myvietnamvisapro.com as they offer quick turn around time and privacy service for vietnam voa letter.
Hue and Hoi An are very beautiful with ancient houses and friendly people. HCMC is very exciting and effervescent. Nothing much to say about HN, I have the feeling of a peaceful city. It's not as exciting as HCMC, but it has it own beauty.
I have never tried Imperial Classic Cruise then I can't help.
Hope my advise works for you
