When I use mine in the boat I just set it down flat on the floor. Haven't had any problems. I also bought the holster, but only use that when I am hunting or walking around. The directions for the Thermacell say to properly use the Thermacell it must be in a horizontal position. I have found it works just as well in the holster attached to my belt or belt loop of my pants. I have found no difference in the operation between vertical and horizontal.
I have a 17 foot boat and found one Thermacell is sufficient, depending on the wind speed, however, two cannot hurt and would give you some overlapping coverage. The Thermacell covers 250 square feet, which is just shy of a 16 X 16 foot area.
You usually will go through the butane faster than the scent pads. I always have a lot of pads left. I order replacement butane from ebay. You will need an adapter for these particular butan cartridges, but the guy I ordered mine from had the adapter and butane as a package deal. When I get a chance later I will post the link for you. I think I paid around $20 for 12 butane cartridges and the adapter.