Ericka,
We started our trip from Amanwana (sometimes they start from Labuanbajo) we sailed the afternoon and the whole night to get to the first island in the strait between Flores and Sumbawa (where Komodo and Rinja are located).
The sea was quite rough, I did not get seasick (I experienced something close to a rollercoaster in the mediterranean so this made me laugh) but some friends did.
From day 2 you sail in this amazing sea with dolphins, huge corals, millions of fishes. There are dozens of islets so there are virtually no waves, just an incredible stream (it's where the sea of Flores merges into the Indian ocean) but the sea was flat as a lake so we felt ok the whole time.
On the way back to Amanwana we decided (by paying an extra fee) to stay some more time on the boat and take a seaplane from Labuanbajo to Moyo and avoided the rough part of sailing back to Amanwana.
The Silolona was Beautiful indeed, but I understand from the website that from 2006 the trip will be done with another boat.
The service was outstanding (17 staff vs. 7 travellers). All indonesians except one english guy from Amanwana. They were all incredibly nice. At the end of the trip we did an amazing dinner with the crew singing local songs with guitars and percussions. The sea is beautiful, the landscape is dry and prehistoric (not only because of the dragons) and not comparable with anything I have ever seen. Last, but not least, the weather is completely different than other places in Indonesia (e.g. Bali). It's very dry so no rain no clouds, if you are tan addicted...

Zigzag,
I was in Bhutan in 2002 (I saw Amankora under construction). That is another absolutely fantastic trip. You will enjoy it for sure. I slept in very simple (so to say...) accommodation, but I can tell you the places and people are so unspoilt that it has been time travelling.