OP, you need to help us out and answer this. I cannot see this answered either. If you do not lock the mechanical advance in the distributor, then it will continue to add advance to the system and the electronic will add even more simulated mechanical advance.
But this possible issue assumes that the new system is measuring crank timing off of a pickup device in the distributor, and does not involve installing a new crank position sensor outside of the distributor.
And when you are driving along, are you monitoring the timing through some electronic device connected to the system?