The increasing complexity of System-on-Chip (SoC) and the ongoing technology miniaturization on Integrated Circuit (IC) manufacturing processes makes modern SoCs more susceptible to Single-Event Effects (SEE) caused by radiation, even at sea level. To provide realistic estimates at a low cost, efficient analysis techniques capable of replicating SEEs are required. Among these methods, fault injection through emulation using Field-Programmable Gate Array (FPGA) enables campaigns to be run on a Circuit Under Test (CUT). This paper investigates the use of an FPGA architecture to speed up the execution of fault campaigns. As a result, a new methodology for mapping the CUT occupation on the FPGA is proposed, significantly reducing the total number of faults to be injected. In addition, a fault injection technique/flow is proposed to demonstrate the benefits of cutting-edge approaches. The presented technique emulates Single-Event Transient (SET) in all combinatorial elements of the CUT using the Internal Configuration Access Port (ICAP) of Xilinx FPGAs.