there is a couple of ways you can do it.
1.) build a divider wall. Depending on roof slope this may or may not work. A simple 2x4 nailed to the deck with a 2x6,8,10 your choice nailed on edge. Flash the Torched side first lap to top of 2x on edge, flash EPDM side last and let it wrap over the top and down the other side 3-4 inchs, cap nail off and put a cap metal on it.
2.) at tie off area on epdm side burry the EPDM under a 2x4 and water stop the heck out of it. then let your torch roof go over the top, making sure not to heat up the rubber. Anchor bar down threw both layers and mastic and membrane the lap. (this is not ideal) but in any case if one side leaks it wont transfer over to the other/new material.
3.) and best option. Use EPDM on the new roof.