How does the stock ECU handle bigger injectors?
 

If you swap out the stock injectors for higher flowing ones, but keep the ECU as is, how does it handle things? Would it be better to get a piggyback system like an SAFC or eManage?

Depends on how much bigger they are than stock. 20% larger than stock will throw a code due to fuel trims maxing out, and depends on whether you can turn down the fuel pressure enough. But, neither case will help you with creating more power on boost.