When operating from a vessel, you will need to consider several factors when designating a launch location.
First has to do with the vessel itself. Are there any snag hazards more prevalent in one area than another? Where is the propeller? Is there a safe place for the tether handler? Are there differences in freeboard (distance from the deck to the water) along the length of the boat? Lower freeboard is generally easier for the tether handler than working from a place with high freeboard.
Next, consider the atmospheric conditions. Where is the wind coming from? Is the wind expected to shift during this mission? Are we expecting a significant change in weather conditions during this mission? Most boats when anchored will lie bow into the wind so either side will be OK. Some boats, however, will be sitting abeam (90 degrees) to the wind. In this case, it is better to launch the sub on the downwind or leeward side of the vessel.
Another consideration is the sea state. What is the strength and direction of the current? What is the height and the direction of the waves? Are you expecting at change of current or sea state during this mission? Ideally, it is better to launch on the down current side of the vessel. If you know there will be a current change due to tide, the best preparation is knowing the time as well as the expected strength and having a mechanism for moving the tether to the other side of the boat or a plan for sub recovery knowing that the sub may be coming back from under the vessel.