I personally like the one with the highest resolution on the trolling motor. That is where you fish and in my opinion where you need more detail. Transom mounts can be tricky depending on the boat and at what speed you want to be able to read the structure. The transducer needs to be mounted so that it is in the water at top speed and where it will receive the least turbulance. Lowrance and probably hummingbird have tips on transducer mounting.
http://www.lowrance.com/support/installation_guide.asp
Location
1. The transducer must be placed in a location that has a smooth flow of water at all times. If the transducer is not placed in a smooth flow of water, interference will show on the sonar’s display in the form of random lines or dots whenever the boat is moving.
2. The transducer should be installed with it’s face pointing straight down, if possible.
3. Make certain the transducer's location doesn’t interfere with the trailer or hauling of the boat. Also, don’t mount it closer than approximately one foot from the engine’s lower unit. This will prevent cavitation interference with the propeller. Typically, the transducer should be mounted as deep in the water as possible. This increases the chance that it will be in the water in high speed and reduces the possibility of air bubble interference.