If you have not taken out the distributor or loosened up the hold-down bolt and turned it you haven't disturbed any engine timing settings.
The relationship of the flywheel to the torque converter does not make any difference, so you have not disturbed the timing. Just make sure the bolts line up and that they are tight. Some flywheels have multiple bolt holes and only one set will line up properly. Its also a good idea to use Locktight or Blue thread locker to keep them from loosening up later on.