Well that is a reasonable fear.
There are ways to help, and they are easy.
I have spent the last 3 hours scouring Google Images and YouTube because I think that a picture is worth a thousand words, and these two videos I have chosen have lots of explanatory pictures.
Perhaps if you view these two videos it may help. At least the second one (maybe the first too) has a short ad at the start, which can be skipped.
The first is at http://youtu.be/nhWU3Ziq80I and shows the exact route I suggest to Zattere from P Roma. The video starts with boarding at Ferrovia - the railway station - which is just across the Grand Canal and down a bit from P Roma, one stop before P Roma. The first boat that comes past the dock is a pointy black one, which is called a Motoscafo and in this case it is probably going to Murano. We catch the next boat which is going the other way, and will be a Number 2 via the Giudecca Canal. The boat approaches an area with lots of trees which the park next to the Sofitel and across a back canal from P Roma, then you see it slow down under the new bridge and then, just before docking at P Roma the video skips past there and the inner area, and the cruise dock, to S Basilio. You then see the Zattere fondamenta approaching and then the film ends as the boat arrives at the dock.
The second video is at http://youtu.be/B1Aqq3_b1fM and it shows the area where the luggage should go and how you can keep an eye on it, although I will say that whenever I throw a piece below the table I don't usually worry too much.
You get a decent view of the type of boat the number 2 is, the wide cream coloured ones. This trip is a number 1 between Rialto and S Silvestro and onwards to S Angelo. You can see that there is an area near the front of the boat, sometimes with forward facing seats and sometimes not, then the Captain's wheelhouse, then directly behind the Captain (visible at the start of the film and as the boat is docked at S Silvestro) an area for luggage with a flat table top and a couple of tubes forming the sides. It is open at the front and that is where you should put any luggage that is not staying with you. Excess can go on the top of the table, or ask the crewperson. They are very busy but if you ask nicely when they are not dealing with the docking - they are far too busy then - they will try to help.
That is in the open (but covered) area where people stand, either because they have a short trip or like the view or are lazy. You can stand there too, and be right next to your luggage if you want. Or stand along the side as long as you are not in the way at docking. Then there is the large cabin with lots of seats on both sides of the aisle, and probably you can find seats which give you a view of your luggage without straining. Don't sit in the seats reserved for disabled unless you fit the categories printed on the seat and the seatback. At the very back of the boat, through swinging doors are a very few rear facing outside seats.
So, we should be able to make it that you can stow your luggage, nobody will make off with your underwear and ball gown, and I expect you to have your most valuable items with you in whatever your airline will allow you to take on the plane, and I'm sure you will have a moneybelt.
I am also sure that you will have purchased tickets (we can talk about what kind after we get this sorted out) and validated them on the machine (I saw another YouTube for that if you need it) before you boarded.
Does this help at all?
Once we get you checked in I will share my favourite places for nibbles around there....
By the way, when is this adventure, where are you arriving from, and what time of day?