Results of modeling with the 3-D STRUCT and MARS15 codes of beam loss localization and related radiation effects are presented for the slipstacking injection to the Fermilab Main Injector. Simulations of proton beam loss are done using multi-turn tracking with realistic accelerator apertures, nonlinear fields in the accelerator magnets and time function of the RF manipulations to explain the results of beam loss measurements. The collimation system consists of one primary and four secondary collimators. It intercepts a beam power of 1.6 kW at a scraping rate of 5% of 5.5E+13 ppp, with a beam loss rate in the ring outside the collimation region of 1 W/m or less. Based on thorough energy deposition and radiation modeling, a corresponding collimator design was developed that satisfies all the radiation and engineering constraints.