Re: I am looking to install a custom stereo in my Bayliner
Did it not come with a stereo system stock?
My best advice is to install all the components in a location that would hinder theft. My friend had boatloads

D) of stereo equipment installed into his boat and it all got jacked while the boat was sitting outside his house. This had to be over a thousand dollars of equipment.
Try to make it as low profile as possible, including the speakers. Maybe you could install the sub under one of the rear seats.
If the glove box is big enough look into installing the head unit in there, and getting a remote control unit to install near the instrument cluster if you need to control it while driving (turning off mute after pulling up a wakeboarder or skier). This is also good because sometimes you may want to appoint a designated DJ to sit in the passenger seat and control the radio at times.
The amps you may be able to mount under the glove box area depending on their size. They should be out of the way so they don't get wet but they also need airflow. If you get a "marine" amplifier the moisture may not be an issue. Try to use some of those screws that you can only tighten but the screwdriver slips off if you turn it the other way (stainless steel of course). (Edit: Even better - get some of these babies -
http://www.amazon.com/IMPERIAL-161411-ANTI-THEFT-SHEET-METAL/dp/B001EVYISY)
When you ask what kind of amp do you need, do you mean a brand or type? You're going to need two; one class D for the sub and one 4 channel for the speakers. Brand is preferential.
I have an old Bayliner project that I already bought the stereo system for, so I'll be working on something like this real soon. Obviously no pics now though, sorry.