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Are both Gmapping and amcl publishing Map to Odom TF? Is there any confliction?

Yes, both are. You wouldn't typically run both at the same time. gmapping performs SLAM (builds a map and localizes simultaneously) while amcl performs localization on a pre-existing map.

The choice of which on to run depends on what you are trying to do. It sounds like maybe you don't want to run either of them, because you're writing your own SLAM system. If that is the case, make sure your SLAM system publishes a map that is usable by the path-planners in the ROS navigation stack. Take a look at map_server for example.