Hi Jacob,

Have you considered using Cytoscape?

http://www.cytoscape.org/

It's quite easy to use and is freely available. It has several pre-made graphical styles to choose from but you can also make your own. If you have an Excel sheet of the interactions formatted as below (where 0 is inhibition, 1 is activation):

Gene-A           0              Gene-B

Gene-B          1              Gene-C

Then you can import this into Cytoscape and it will generate a network image based on that. It is possible to drag by hand and re-order any of the network constituents but under the Layout tab Cytoscape has a few pre-defined layouts based on the properties of your network, so you can also try those.

Hope this helps.