In honesty, you don't need to use the binary converter for the mod to run. The whole purpose of it is to improve loading time.
As for having the Mod show up in your game's list, here's some pitfalls that I've seen that may help you:
If you modify or add any file(s) in a folder (Game Info, Mesh, etc), you must copy the entire folder to your Mod's directory. Ex: Your mod named "Super Kol" has only one change, the Kol cap ship has more Armor. Since you modified the Kol's file, you must copy the entire Game Info folder from the Reference Data into your mod's directory. Supposedly this will change in 1.03, but it's still important to know.
The other big pitfall is the placement of your mod directory. We'll take "Super Kol" again just for prosperity. In game I click on the Mod Path button and it shows me
"C:\Documents and Settings\{Your user name]\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Mods"
With that, I can browse to that location. Just remember that it's Local Settings\Application Data, both of which are hidden folders. You'll either need to type the path in, or have your windows show hidden folders. Once I get there I create a new folder and name it what I want to display in the SINS mod list (Super Kol). In that directory is where I place my folders. Doing all of that, my Super Kol mod shows up in the Mod List.
I don't have Vista so I don't know the path for it. you'll just have to find out in game.