Setting your STB to 1080i is right for hd, but if you watch sd through the STB you will not be able to access all the screen modes. Some STB's such as the Motorolas let you set the box to pass pictures in a native 480i resolution to the set in either 480i or 480p, while sending 720p or 1080i shows at 1080i. This is better than setting everything to 1080i. You can select to view signals received via component or HDMI at 480p at either 540p or 1080i; I can't see much difference between the two.
If your STB that all channels, both native sd and hd broadcasts, be set at a single resolution, then (1) set the STB at 1080i, and (2) use a splitter and watch channels 2-100 using the tv's tuner.