According to the news page on Inkscape one of the features that was added to was

Raster Functionality. Hooks in ImageMagick for use in Inkscape for bitmap effects.

My question is what is how do you make the two work together? I am only familar with programs in which I have a window and then basically work from the menu. Imagemagick appears to be only a command line program is that correct?

Yes, that's correct. ImageMagick is a command line program. You specify input image(s), various arguments that define modifications, and then it produces output image(s).

From what I understand, you won't need to worry about that yourself. Inkscape will just use ImageMagick behind the scenes for various operations, so they don't have to write the code for Inkscape. The fact that ImageMagick is a command line program makes it easier to use for behind-the-scenes stuff like this, and it is already stable and well regarded.