Measure measure measure and measure again. Spend some time with the cardboard template for cutting on the side of your case and make sure you like the shape and positioning. I'd keep the window away from the front drive cages and possibly just above your PSU to help hide cabling etc. I like the job some people do of putting another plate between the PSU and the motherboard to really create a separation visually. I'd play around with a bunch of configurations, all in a cardboard/chipboard material and really try some different options out.
Try to plan how you will wrap the edge of any cuts in the metal that you make. You can find thin rubber/plastic weather stripping that is shaped like a U that will hold to the edge very well.
If you use screws/bolts to attach the window panel, I'd again try some different layouts of where the screw heads land are and think about materials/color options for that as well, you can really add a lot of punch to the look or make it more subtle.
And most importantly when dealing with thin sheet metal cuts, watch out for your hands. That stuff cuts more easily than a samurai sword, I swear.