manual ecu/auto trans?

Ok heres the deal, I am planning on swapping heads within the next couple weeks and running obd1. I have a chipped p30 ecu and need to know if I can run it with my auto trans for now? I have a maual trans but need to gather the rest of the parts to do the conversion. I know that an auto ecu will not run right with a manual trans but would it be the same if I ran a manual ecu with an auto trans?
 
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