The MAIN thing in saltwater use is to have the right bottom paint, and keep it maintained. Gluvit and other such coatings are good for protection from electrolysis, however, they may not provide protection from marine growth. And anywhere marine growth can attach and leave its calcium deposit, it becomes alkaline, and begins to eat through the coating, and then into the aluminum.
That's where anti-fouling paint comes in. For aluminum boats, you MUST use copper thiocyanate, NOT cuprous oxide. If you use the wrong paint, it will destroy your hull. Look for "Trilux33" in the interlux brand, or if it is another brand, make certain it says that it's formulated for use on aluminum, Specifically, look at the active ingredient and make sure it's not cuprous oxide.
But just putting that directly on your hull won't last long. It is imperative that you use a high quality 2-part epoxy primer, for use below the waterline. Interlux interprotect fits this bill nicely. (I'm not a salesman for the company, I just like this brand) Apply 2-3 coats, then apply your antifouling paint, gluvit, or other coating.
You should also have galvanic protection in the form of zinc anodes. Yes, your outboard has them, usually one on the lower unit, and on larger motors, there is one under the PT unit. HOWEVER, these are to protect the motor, there is not enough surface area of these anodes to afford any protection of your hull. Therefore, you should mount an anode to your transom. Mount it below the static flow waterline, where it will be submerged when the boat is at rest.
Here's the easy way: Using a set of bolts, washers, and nylock nuts, you place the bolts through the hull from the inside with one washer, and then place one washer and nut on the outside and tighten. Use RTV Ultra Black, or 3M 5200 on the washers. Use a bolt long enough so that after you tighten down the outside nut, you still have about 2" of thread protruding. This will form your mounting 'studs' Next, you will use a strip of 1/8" aluminum plate, about 2" wide, and long enough to cover the distance between studs, with a little extra beyond the stud. This is where you will drill mount holes. Your strip will then fit over the 'studs' and you use a set of lock nuts to secure the strip in place. Last, you will drill another set of holes in this aluminum strip, to correspond with your anode mount holes. Place the anode between the transom and the backer plate, with the fastener from the inside of the anode, through the backer plate, so the nut, and any protruding bolt end faces away from the transom, rather than gouging into it. Use a large set of bolts, nuts, and washers for this. I recommend 3/8" diameter
Your bolt mount pattern will depend on the anode you select, obviously. But the idea is that rather than having to remove bolts, and re-do them with sealant every time you remove the anode from the transom, you simply loosen the 2 nuts that hold the aluminum backer plate to the studs sticking out the transom, then remove the strip, remove the anode, replace, and re-attach.
Also, with the backer plate, it reduces the chances of erosion of the anode allowing it to fall off a small fastener and leave the boat with no protection.
Make sure to run a bonding wire from your transom anode to the PT anode (if available) or, to the negative terminal of your battery (if so equipped) For boats with no battery, electrolysis is less of an issue to begin with, and there is no stray current to deal with, so, simply having the anode bolted up to the hull will be sufficient.
Let me know if you want pics showing detail of this setup, I can take some pics of my Triton 1650.
Lastly...bunks. A lot of people use carpeted bunks. I do, as well. As long as you have good bottom paint, and you are keeping an eye on its condition, and you make sure to thoroughly rinse your trailer and boat (including the underside of the boat, especially where the bunk carpet touches, saturate that carpet with fresh water) then, you shouldn't have many problems with this.
Hope this info helps.