The MegaSquirt 1 and 2 ECUs seem to have only four injector output pins (or terminals on the relay board) but they are labeled as pairs so this is even more confusing, do I have two or four injector outputs? And how does either two or four outputs allow me to run 6, 8, or 12 injectors?

With the MS1 and MS2 you have two ‘banks’ or groups of injectors.  You can use one or both of them. With 1-6 cylinders one is fine, though you can use both and generally would do so unless you were using the second bank for a different purpose, such as staged injection. With more than six you should share the load across both banks. 

Each bank has two terminals that you bring together to a nice fat (i.e. 14ga) wire that goes out to all of the injectors on that bank. For an 8cyl example you might choose to run two banks of 4 injectors each. You’ll run 12v to one side of all eight injectors that are hot in the ‘crank’ and ‘run’ positions. Similarly, you’ll run the 14ga wire out from one pair of terminals (one injector bank output) nearby the injectors where you’ll split that 14ga off into 4 smaller gauge (20ga likely) short wire runs to the individual injectors. Do the same thing for the other bank.

For sensor & wiring diagrams, please visit http://www.msextra.com/manuals/schematics/

Note that when running a MegaSquirt-III, you can still run batch injection if you choose, using the same wiring diagram as above.  However you can also purchase your MegaSquirt-III with the MS3X Expander Board, and then have up to 8 channels of sequential fuel and ignition outputs available.  (Not to mention all of the other features this enables, lots of I/O).

Check out the MS3X Wiring Diagram here.