PS: What's the real point of powering the SS from the +5 header and not usb? Is it just for using smoothstepper to power break-out boards that require more than 500mA? Also, as a 2nd side note, under what circumstances would I want to ground it, I thought it was to eliminate ground loops (grounded all of my power supplies at the same point)
The way the SmoothStepper is configured a USB port will only give it 100 ma of current. Some computers can have a tough time supplying the proper amount of current or voltage level to USB devices. This combined with some USB cables that have 28 AWG power leads can lead to problems. I built a custom controller for a company that used two USB devices so it had an internal hub. The current draw of all three devices was only about 250ma or so but it was enough to cause a significant voltage drop across a 6' USB cable that had 28 AWG power leads. A more stout cable solved the issue. As you mentioned another good cause for using an external power supply is when using BOBs that steal power from the SS.
As for your second question first let's clear up that DC Common, (i.e. negative, -), is not the same thing as Earth Ground. DC Common is the common return path for DC circuits. For example, your PC has a power supply that outputs +5V, +12V both of these voltage share the same DC Common (which is typically referred to as 'ground'). If you take a volt meter and measure from DC Common to the 5V output you get 5V, and from DC Common to the 12V output you would see 12V. It is the common current return path for each circuit.
Earth Ground is actually a connection to the Earth outside your home/shop. It's purpose is to increase safety and secondary provide a low impedance path to bleed of noise. It is NOT a current carrying path for your circuits. It is common practice to (earth)ground each sub assembly back to a common point and then to bond that point to your electrical systems (earth)ground. For example a DC power supply typically has an (earth)ground terminal that connects to its case. This (earth)ground connection helps to bleeds off electrical noise that might otherwise be radiated by the power supply but more importantly if insures that the case of the power supply will never go above ground potential and be a shock hazard. You do not want to go around connecting DC Commons to (earth)grounds unless you have a very compelling reason.
A ground loop is created when a voltage difference is created between two devices due to current flowing through a ground connection. For instance if you daisy chain an (earth)ground instead of star grounding it. Many power supplies will have the DC Common bonded to (earth)ground inside of them, if you create separate (earth)ground externally you could potentially create a ground loop by providing a path for DC current to flow through the (earth)ground.
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