svg2mod is a standalone python tool. It needs to be run from a termainl (console, command-line, whatever you want to call it)
Make sure you have python installed.
(for linux just install python with you package manager. Version 2.7.x and 3.x should be ok for svg2mod)
go to the github page of svg2mod
select clone or download and download as zip
unpack the zip (and remember where you placed it.)
download the svg file i provided above. (remember where you placed it. The simplest for you would be to place it in the directory of svg2mod)
Now my lack of knowledge about windows becomes apparent.
Here a explanation how to rund python scripts under windows: http://pythoncentral.io/execute-python-script-file-shell/
open a terminal (cmd in windows i think)
Navigate to the directory holding svg2mod (there is a svg2mod.py file) The cd commad is used to change the directory. ls to few the contents (dir in windows)
If you are in the correct directory and have the svg file in the same directory simply enter the following:
Linux: python ./svg2mod.py --format pretty -p 0.1 -i ./Arduino_Logo_silk_10x10mm.svg -o ./Arduino_Logo_silk_10x10mm
Windows: [path to the python binary] ./svg2mod.py --format pretty -p 0.1 -i ./Arduino_Logo_silk_10x10mm.svg -o ./Arduino_Logo_silk_10x10mm
[path to the python binary] depends on your installation.
A standard installation puts it under: C:\Python27\python.exe
This would produce a 10x8mm logo on f.silks (because that is how i created the svg file)
If you want a different size simply add a scaling factor (-f [scale])
example to get a 5x4mm logo:
python ./svg2mod.py --format pretty -f 0.5 -p 0.1 -i ./Arduino_Logo_silk_10x10mm.svg -o ./Arduino_Logo_silk_10x10mm
If you want the logo on another layer open the svg file in inkscape and either rename the layer it is on or move it to another layer. (I provided you with the layers for mask and copper already.) To move stuff to another layer: select it. Right click->move to layer. Select the layer you want.
Look in the document properties. There you can set the background color. (Normally it is transparent as you already discovered)
The document properties are under file->document properties
(again replace python with [path to python binary] on windows)