Most of this is covered in the tutorial, but here it is anyway.
MulTool can do a variety of things, but most useful for map making is Freezing and Clearing of Statics.
It is recommended that the other portions of the program not be used.
Melting:
Enter the paths to your statics0.mul, staidx0.mul and to where you want the items.wsc (this can be renamed) to be placed.
Item start/type: This is the item type that will be melted into the item.wsc. The default is 0 255, and will melt everything in the area defined below. Set to 255 255 to only melt item type 255.
Coordinates:
X1 and Y1: This is the upper left corner of the area to melt.
X2 and Y2: This is the lower right corner of the area to melt.
Placed where:
X and Y: This is where you want the items placed. If you are not moving it, then they should match X1 and Y1.
Z: This is an offset value if you are moving the items. This would be relative.
NOTE: This does not erase the statics like WorldForge. Use the clear statics (next)
Clearing:
This is pretty simple. Put the paths in and the area you want to clear.
X1 and Y1 are the upper left corner and X2 and Y2 are the lower right corner.
Freezing:
Enter the paths accordingly. Enter the item type you want froze, or check the
All box to freeze everything.