You can use a German Rail Pass day so that you can ride the boat for free. Getting on the boat at Mainz at 8:45 is the only way you can make it the entire journey to Cologne in one day. Getting on at Mainz means you get your choice of spots as well because many people do not board until later (there isn't much to see for about an hour). After Koblenz there isn't very much to see so it might not be worth going past that location.
You can bring luggage onto the boat. On the lowest level below the steps there is luggage storage but it isn't locked so use at your own risk. You cannot bring luggage into the dining room but you can bring it to the very top deck if you don't want to leave it unattended. There is some small snacks available on the top deck, and the food in the dining room is good but can be expensive for some items. The dining room (even when it's not busy) can take quite a bit for you to get food at- it took my brother 40 minutes to get a bowl of pasta with the dining room only having about 7 tables with people at them.
If you want to make sure people don't jump in front of you to take pictures sit on the right side of the boat (leaving Mainz) along the railing as more is on the right then on the left.
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