Here's what I think happened: I think KM drove the Toyota back while FD had his own Chevy Suburban in New Canaan (to which he transferred JFD's body). FD expected that KM would dispose of the bags of bloody paper towels which KM had transferred to the Toyota after driving JFD's Suburban (after body handoff and FD Suburban handoff) to Lapham Rd where the Toyota was parked. When FD and MT later arrived at 80 MS Rd, they discovered the bags of bloody paper towels in the Toyota.
The bags of bloody paper towels were not part of the conspiracy plan, but happened because JFD fought back more than anticipated. So, the plan didn't account for anyone disposing of the bags of bloody paper towels. KM didn't do it, so FD and MT had to once they discovered them in the Toyota. Burning them in the east fireplace of 4JC was an improvisation.