It sounds like you have created a revesing section. That requires special wiring, whether its DC or DCC.
Easy solution is to put insulated rail joiners on all 4 rails where the connecting track joins to the switches and then buy an automatic reverser unit ($30-50) and install it between the reversing section and the rest of the railroad.
Slightly more complicated solution, but much cheaper, more old school and not as user friendly, is to install the insulated joiners and install a DPDT toggle switch between the connecting track and the rest of the railroad. That will require you to keep track of which end the train is entering from and throw the switch while the train is on the connecting track, every time the train passes throught eh connecting track.
Dave H. Painted side goes up. My website : wnbranch.com
Marlon
See pictures of the Clinton-Golden Valley RR