200kHz is a narrower beam than 50kHz. If you want fine detail, use 200. If you want the "big picture", use 50kHz. Many sounders have a splitscreen view which show both. I also find that the bottom makes a fair bit of difference - mud reflects differently than sand, etc.
As to thruhull or transom, thruhull is probably better. If you have a non-cored fiberglass bottom, you may be able to mount in the bilge, and "shoot through" the hull, which is probably the most reliable.
If transom, just mount where you have the best vertical shot.