Megasquirt is an inexpensive stand alone ECU that you assemble your self. Bikirom is a daughterboard that you solder into your ECU and it comes with software that allows you to tune.
Most people are of the opinion that piggybacks can be problematic for the following reason.
Your ECU bases the injectors pulse width on load & RPM. There is a global formula for this and then adjustments are made based on info contained in a spread sheet that plots engine load against RPM. Piggiebacks alter this global setting according to the new injector size, typically cutting it in half. This changes the base pulse width (TP) to give an A/F ratio that is basically stoich but can cause the ECU to look to the wrong areas of the map. Where this is especially problematic is timing.
Bottom line, the Bikirom costs less than the Emanage if I'm not mistaken and will allow you to tune properly. Even if you only use it to tune fuel and use a BTM for boost retard it is worth doing.
If you're a DIY kind of guy, check out
http://www.hybridka.com. There is info on fitting your ECU with a daughterboard and all that stuff.