Verdite is probably the expert on this, but as far as I know, there are two ways to add water to a map- as a Map Piece or as an Object.
Using Map Piece water is FAR easier for large bodies of water, but Map Pieces don't support semi-transparent textures so they look solid. They're placed on the map just like any other map Piece tile would be.
When using Object water, it can be translucent. but you have to place a lot of separate water Objects if you are making a large body of water. SoM has a cap on the maximum number of object for each map, so they are suitable mostly for rivers, puddles or ponds etc. Sorry that the water sheets on that site are messy; they were one of the earliest things I made so I didn't even know what I was doing
The .MDO and .TXR files go in the "...\DATA\OBJ\MODEL" folder, and the rest (PRF files) go in "...\DATA\OBJ\prof" folder. After that, they should show up in the Parameter editor on the "OBJECTS" tab named "(who would have guessed!) "Water..." Your best bet is to use the water Object named "Water 2mx2m", but the name is actually wrong. They are technically 6m x 6m. An "m" is roughly one meter in-game. Each map Piece tile is 2mx2m. So you would place a water Object on every third map Piece to have them join each other seamlessly. The water sheets are set low to around -1m by default.
Attached is a picture of water Objects as Placed on a map. Notice the "every third" spacing of the green Object dots.
And also also an ingame picture of water map Pieces (opaque) to show what they would be like. 
Using Map Piece water is FAR easier for large bodies of water, but Map Pieces don't support semi-transparent textures so they look solid. They're placed on the map just like any other map Piece tile would be.
When using Object water, it can be translucent. but you have to place a lot of separate water Objects if you are making a large body of water. SoM has a cap on the maximum number of object for each map, so they are suitable mostly for rivers, puddles or ponds etc. Sorry that the water sheets on that site are messy; they were one of the earliest things I made so I didn't even know what I was doing
The .MDO and .TXR files go in the "...\DATA\OBJ\MODEL" folder, and the rest (PRF files) go in "...\DATA\OBJ\prof" folder. After that, they should show up in the Parameter editor on the "OBJECTS" tab named "(who would have guessed!) "Water..." Your best bet is to use the water Object named "Water 2mx2m", but the name is actually wrong. They are technically 6m x 6m. An "m" is roughly one meter in-game. Each map Piece tile is 2mx2m. So you would place a water Object on every third map Piece to have them join each other seamlessly. The water sheets are set low to around -1m by default.Attached is a picture of water Objects as Placed on a map. Notice the "every third" spacing of the green Object dots.
And also also an ingame picture of water map Pieces (opaque) to show what they would be like.