the extra injector's ar normally only used on boosted car's and are run from a pressure sensor in the boost pipe, higher boost + more fuel = more power.
The injectors are pulse width modulated, so a longer pulse = more fuel.
one side of each injector is connected to igition + (12v), and the other is grounded via the ecu, to provide the opening pulses.
adding an extra injector is easy, with sensors readily available, and the most basic pic processor capable of doing the conversion from voltage to pwm and can also add some safety features with the spare pins.
if your serious about building your own ecu, i suggest that you visit
www.megasquirt.info, build one of there ecus and learn how it all works, and then (if you successfully get your car running on the megasquirt), proceed to building something of your own with the features you need.
be prepared to buy new injectors along the way, as they are different impedence between different cars, and can be damaged by wrong wiring.
and if you screw up, and run lean, its gonna blow your engine too. not trying to put you off, just want you to realise how big a job this is.