the vaseline is a good tip. if you don't want to glue or Goop, and might want to remove the transducer for use in another boat or if you ever sell the boat, removal is so simple.
in a previous life, i worked with industrial ultrasound, lemme give you a quick lesson that might help you understand why transducers do what they do and what to look out for in mounting, and dispel a thing or two.
a fishing transducer works just like the ultrasound you get in the hospital. same principal, just a few character differences.
ultrasound--the 'sound' the transducer makes, cannot travel through air. it has to pass through a liquid, gel, or solid. yes, it can easily move through a solid--even as dense as lead or gold, and steel is a very comfortable medium for ultrasound to move right through. if it hits air, it stops--or bounces back to the xducer.
"but, i can hear my transducer clicking". you hear the crystals 'clicking', but you dont hear the ultrasound.
the xducer usually has two crystals in it--one sends one receives (usually two, sometimes only one to do both jobs. higher end units have 2). and by crystal, it is actually a wafer thin slice of a crystal, usually a lithium material. they both vibrate and you can hear them 'clicking'. you can even feel the pulses if you hold your finger on the bottom side.
rumor one--it's bad for your transducer to 'click' out of water. well, not really. i suppose after a very very long time the crystals could vibrate enough to create heat and cause damage? so, dont leave your machine on for days on end.
but if the sound can travel through solids or liquids, why can i 'see' the fish, the bottom, the rocks, thermoclines and other stuff. those are solids and liquids, right? right. i dont want to change everyones way of thinking, but actually the sound does not really 'bounce' off objects and come back. in a nutshell, the sound changes speed when it hits objects of different density-like passing thru water and then thru a rock. different densities. when you are driving down the interstate and you hit a deep puddle--your car suddenly slows down, and then speeds up again when you get through the puddle. scary, but sort of the same thing. the tires hit something of a different density and had to change velocity.
your high-end fishfinder detects the differences in the velocity of the sound and calculates it as a signal on your screen. (a DSI machine, for instance, does some crazy math and can detect some insane velocity changes and calculate those into photo-real images)
super tech word buzz--the crystals in your xducer take electrical energy from your machine, and changes this to mechanical energy. the mechanical energy is the clicking and sending out the ultrasound out. when the sound bounces back, the crystal vibrates and then changes this mechanical energy to electrical signals and sends it to your display. this is called a piezoelectrical effect.
rumor two--a transducer that is mounted to shoot-thu is not sensitive and might not be accurate. or--you can 'see' the hull on the display. not, not really. the difference in signal in this type of equipment is so small, a normal human or hobbit or syrian dictator would never be able to discern. if you think you can tell a difference, congratulations. i wont argue, but science is science. what you will lose is temp or speed or whatever other features your xducer has built in.
super tech word buzz--the reason you dont 'see' the hull or why the shoot-thru makes no real difference is the 'dead zone', which is an area where the crystal is vibrating to send the signs--then pause--and then vibrate when a signal returns to it. (rough explanation, no critics please). and in a fish finder transducer, this dead zone is probably a foot or so. every wonder why you can't see the 'bottom', when you put your transducer in a bucket in the drive way? yea. that's the reason.
"its not deep enough" is a good enough answer, but to dazzle the biches... "why yes, this particular diameter piezoelectrical crystal with regard to its frequency, creates an elongated near-field producing a dead zone greater than the distance of the medium in the vessel." biches love science.
rumor three--if there is an air bubble in the mounting medium, your machine will not work. well, yes and no. the whole 'ultrasound can't pass thru air' thing comes into play, so yea, this could be true, but then add the near field thing and a guy named Fresnel, and it should be a 'no'. but, the air can be the more powerful force here, and it 'could' cause an issue. but...a couple of tiny bubbles are going to make NO difference. be careful, but dont be afraid to use marine Goop to put the transducer in place. a dozen tiny pinhead sized bubbles, 'should' cause no visible affect.
so, if you are still awake after all that, you might have learned a couple of things--you can mount your transducer in a liquid, a solid, or a gel, but not air. if you mount it shoot-thru, then you can't have air anyplace underneath the sound path. as long as there is a dense material under the xducer, then you should be very happy with the results. but, do be careful there are a minimum of air bubbles in your permanent mounting medium. that's why most tech-tips say to press and twist--to press out the bubbles. you can use a water bath to place the xducer in, or you can use vaseline, KY, green jello or camel's milk. as long as it's liquid or solid.
personally i prefer directly in the water. all my powerboats have-and have had, the transducers mounted in direct contact with the water. in the Hobie PA14, the DSI transducer is rigid mounted with Goop, in the hull just aft of the mast support. this was what my lil fishing buddy wanted, so that's what we did. i can pick fly poop out of pepper with this unit. the only drawback is not having water temp. in the PA12, i used the Lowrance-ready set up and have the same badass results, and i have the temp.