Whenever I click edit flags from the pandemic tools, nothing happens.
I am using the Autodesk student version of Softimage 2013 if that helps.

The Pandemic Tools are not compatible with any version of the free XSI Mod Tool or full commercial versions of XSI 6 or higher. You'll need to use ANDE's XSI ZETools for those, more information can be found here.

Ok got them

When using edit flags and the like with xsi, there are some things that work best in xsi itself, and others that work best through hexediting. For example, specular, environment map, and scrolling textures all work best in softimage. However, its a lot easier to add glow and transparency via a hexeditor. To learn how to use these, I recommend D.A.R.T.H.D.U.C.K's tutorial HERE, and I recommend the following hexeditor: XVI32.

ok I'll have a look at that, thanks!

Edit: I have the tool but I am quite new on how to use it. (okay I'm clueless)

I understood that I had to apply a (few) special texture(s) to it + an alpha to get it to be see through.
2 things:
1. hardedge transparency and additive transparency, do I need both?

2. How do I add an alpha in gimp?

First of all, if you're just adding transparency to a msh, you don't have to do anything to the msh with ZE tools, you just have to export it. Hard-edged is what you want if you're making something that you don't really want to glow, like a window. Additive transparency has a slight glow to it, so use it for things like holograms or energy blades.

Finally, to add an alpha channel in gimp, take your completed texture and go to Colors->Components->Decompose, and select RGB and make sure the layers box is unchecked. You'll then get 3 windows, greyscaled versions of the original. Make a new texture the same size, and copy the original or one of the grey versions into that window. This image will be your alpha channel. Basically, everything that's white will be visible, and black won't be, and grey is in-between. Once you have the new window colored correctly, go to Colors->Components->Compose(or Recompose, something like that), select RGBA, and Alpha is the one you just made, Red is the last one on the list, Green is second to last, and Blue is the top. If it composes and looks bizarre, you got the RGB's backwards, just go back to the individual frames and compose them in the opposite order.

Hope that helps!

wonderful help